8yhz

The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide

Method: X-RAY DIFFRACTION D_max: 81.6 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium channel protein type 9 subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 764–774	Not recorded	Light chain of 1080 Fab × 1 Heavy chain of 1080 Fab × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2M potassium thiocyanate, 25% W/V Polyethylene glycol 3,350	Resolution 1.62 Å R-free 0.210

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8YHZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21TP Open-state structure of veratridine-activated human Nav1.7 Deposited 2025-12-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 Y01 CHOLESTEROL HEMISUCCINATE × 4 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 A1E26 Veratridine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
21TQ The structure of Nav1.7 with veratridine standing near the IFM motif (site I) Deposited 2025-12-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 A1E26 Veratridine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 4 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 P3X (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
5EK0 Human Nav1.7-VSD4-NavAb in complex with GX-936. Deposited 2015-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1527–1559（33 aa） Chain A 1581–1622（42 aa） Chain B 1527–1559（33 aa） Chain B 1581–1622（42 aa） Chain C 1527–1559（33 aa） Chain C 1581–1622（42 aa） Chain D 1527–1559（33 aa） Chain D 1581–1622（42 aa）	Not recorded	PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 21 5P2 3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；277 K；2.2 ammonium sulfate, 100 mM sodium citrate pH 5.4	Resolution 3.53 Å R-free 0.272
6J8G Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (Y1755 up) Deposited 2019-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6J8H Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (Y1755 down) Deposited 2019-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6J8I Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (Y1755 up) Deposited 2019-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9SR (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name) × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6J8J Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (Y1755 down) Deposited 2019-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9SR (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name) × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6N4Q CryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 747–777（31 aa） Chain A 811–842（32 aa） Chain B 747–777（31 aa） Chain B 811–842（32 aa） Chain C 747–777（31 aa） Chain C 811–842（32 aa） Chain D 747–777（31 aa） Chain D 811–842（32 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；10 mM Tris pH 8.0, 100 mM NaCl, 0.06% FA3, 0.1 mg/ml POPC:POPE:POPG mixed at molar ratio 3:1:1 cryo-EM vitrification conditions Cryogen ETHANE；Apply 3 uL, blot 2.5s. Ted Pella 595 filter paper.	Resolution 3.60 Å
6N4R CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 747–777（31 aa） Chain A 811–842（32 aa） Chain B 747–777（31 aa） Chain B 811–842（32 aa） Chain C 747–777（31 aa） Chain C 811–842（32 aa） Chain D 747–777（31 aa） Chain D 811–842（32 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；10 mM Tris pH 8.0, 100 mM NaCl, 0.06% FA3, 0.1 mg/ml POPC:POPE:POPG mixed at molar ratio 3:1:1 cryo-EM vitrification conditions Cryogen ETHANE；Apply 3 uL, blot 2.5s. Ted Pella 595 filter paper.	Resolution 4.20 Å
6NT3 Cryo-EM structure of a human-cockroach hybrid Nav channel. Deposited 2019-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1500–1631（132 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 Y01 CHOLESTEROL HEMISUCCINATE × 1 76F (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate × 4 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 AJP Digitonin × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6NT4 Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2. Deposited 2019-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1500–1631（132 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 76F (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate × 5 AJP Digitonin × 1 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6VXO NaChBac-Nav1.7VSDII chimera in nanodisc Deposited 2020-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 817–832（16 aa） Chain C 817–832（16 aa） Chain D 817–832（16 aa） Chain E 817–832（16 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 3.50 Å
6W6O NaChBac-Nav1.7VSDII chimera and HWTX-IV complex Deposited 2020-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain A 817–832（16 aa） Chain D 817–832（16 aa） Chain F 817–832（16 aa） Chain H 817–832（16 aa）	Not recorded	POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 10 cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 5 seconds before plunging	Resolution 3.20 Å
7K48 Structure of NavAb/Nav1.7-VS2A chimera trapped in the resting state by tarantula toxin m3-Huwentoxin-IV Deposited 2020-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain A 739–779（41 aa） Chain A 805–830（26 aa） Chain B 739–779（41 aa） Chain B 805–830（26 aa） Chain C 739–779（41 aa） Chain C 805–830（26 aa） Chain D 739–779（41 aa） Chain D 805–830（26 aa）	Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2.5-4.0 seconds before plunging	Resolution 3.60 Å
7W9K Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution Deposited 2021-12-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 15 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å
7W9L Cryo-EM structure of human Nav1.7(E406K)-beta1-beta2 complex Deposited 2021-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Mutation：E406K	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 14 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7W9M Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (S6IV pi helix conformer) Deposited 2021-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Mutation：E406K	9SR (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name) × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 5 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7W9P Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV pi helix conformer) Deposited 2021-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Mutation：E406K	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 13 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7W9T Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV alpha helix conformer) Deposited 2021-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Mutation：E406K	9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 5 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 14 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7XM9 Cryo-EM structure of human NaV1.7/beta1/beta2-XEN907 Deposited 2022-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1977（1977 aa）	Mutation：W1150R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 G2E (7~{R})-1'-pentylspiro[6~{H}-furo[3,2-f][1,3]benzodioxole-7,3'-indole]-2'-one × 1 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
7XMF Cryo-EM structure of human NaV1.7/beta1/beta2-Nav1.7-IN2 Deposited 2022-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1977（1977 aa）	Mutation：W1150R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 G2W 3-[[4-[3-(4-fluoranyl-2-methyl-phenoxy)azetidin-1-yl]pyrimidin-2-yl]amino]-~{N}-methyl-benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
7XMG Cryo-EM structure of human NaV1.7/beta1/beta2-TCN-1752 Deposited 2022-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1977（1977 aa）	Mutation：W1150R	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 G4I (1~{Z})-~{N}-[2-methyl-3-[(~{E})-[6-[4-[[4-(trifluoromethyloxy)phenyl]methoxy]piperidin-1-yl]-1~{H}-1,3,5-triazin-2-ylidene]amino]phenyl]ethanimidic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
7XVE Human Nav1.7 mutant class-I Deposited 2022-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Mutation：E156K,G779R,L866F,T870M,A874F,V947F,M952F,V953F,V1438I,V1439F,G1454C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 Y01 CHOLESTEROL HEMISUCCINATE × 1 CLR CHOLESTEROL × 4 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 18 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7XVF Nav1.7 mutant class2 Deposited 2022-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Mutation：E156K,G779R,L866F,T870M,A874F,V947F,M952F,V953F,V1438I,V1439F,G1454C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 Y01 CHOLESTEROL HEMISUCCINATE × 5 CLR CHOLESTEROL × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 17 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8F0P Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-1305 Deposited 2022-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1630（130 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 5 Y01 CHOLESTEROL HEMISUCCINATE × 1 X7L N-[6-(cyclopentylmethoxy)-1,3-benzothiazol-2-yl]-4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å
8F0Q Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the acylsulfonamide inhibitor GDC-0310 Deposited 2022-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1630（130 aa）	Not recorded	BMA beta-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X7R 5-cyclopropyl-4-({1-[(1S)-1-(3,5-dichlorophenyl)ethyl]piperidin-4-yl}methoxy)-2-fluoro-N-(methanesulfonyl)benzamide × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 5 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
8F0R Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the arylsulfonamide inhibitor GNE-3565 Deposited 2022-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1501–1630（130 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X7W 5-chloro-4-({(1S,2S,4S)-2-(dimethylamino)-4-[3-(trifluoromethyl)phenyl]cyclohexyl}amino)-2-fluoro-N-(pyrimidin-4-yl)benzene-1-sulfonamide × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8F0S Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296 Deposited 2022-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1501–1630（130 aa） Fragment：Chimeric construct of human Nav1.7 VSD4 and the NavPaS channel from American cockroach Periplaneta americana	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X80 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8G1A Cryo-EM structure of Nav1.7 with CBD Deposited 2023-02-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 P0T cannabidiol × 2 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 5 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 13 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8I5B Structure of human Nav1.7 in complex with bupivacaine Deposited 2023-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 OJ0 Levobupivacaine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8I5G Structure of human Nav1.7 in complex with PF-05089771 Deposited 2023-01-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 2 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 T70 PF-05089771 × 1 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8I5X Structure of human Nav1.7 in complex with Vinpocetine Deposited 2023-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 5 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 T7F Vinpocetine × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 11 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8I5Y Structure of human Nav1.7 in complex with vixotrigine Deposited 2023-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 4 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 TB4 Vixotrigine × 1 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 14 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8J4F Structure of human Nav1.7 in complex with Hardwickii acid Deposited 2023-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 UK0 (4~{a}~{R},5~{S},6~{R},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid × 1 Y01 CHOLESTEROL HEMISUCCINATE × 3 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 10 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8S9B Cryo-EM structure of Nav1.7 with LCM Deposited 2023-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 LQO lacosamide × 2 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 4 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8S9C Cryo-EM structure of Nav1.7 with CBZ Deposited 2023-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 N6W benzo[b][1]benzazepine-11-carboxamide × 1 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 5 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8THG Cryo-EM structure of Nav1.7 with RLZ Deposited 2023-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 657 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 3 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8THH Cryo-EM structure of Nav1.7 with LTG Deposited 2023-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 IYJ (6M)-6-(2,3-dichlorophenyl)-1,2,4-triazine-3,5-diamine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 4 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8XMM Voltage-gated sodium channel Nav1.7 variant M9 Deposited 2023-12-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CLR CHOLESTEROL × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
8XMN Voltage-gated sodium channel Nav1.7 variant M2 Deposited 2023-12-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
8XMO Voltage-gated sodium channel Nav1.7 variant M4 Deposited 2023-12-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 7 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9ITI Nav1.7 with mutations that eliminate beta1 binding Deposited 2024-07-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1988（1988 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 10 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Y01 CHOLESTEROL HEMISUCCINATE × 4 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å

42 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SCN9A_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–11； UniProt 764–774

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8yhz
Deposition date deposition_date	2024-02-28
Structure title title	The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide
Keywords keywords	inhibitor, NaV1.7, MEMBRANE PROTEIN/IMMUNE SYSTEM, MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.10 Å
Radius of gyration Rg (electron density) rg_electron	24.16 Å
Forward intensity I(0) i0	38448500.00
Molecular weight molecular_weight	47060.0 kDa
Excluded volume excluded_volume	58522 Å³
Envelope volume envelope_volume	71504 Å³
Hydration-shell volume shell_volume	24909 Å³
Envelope diameter envelope_diameter	84.5 Å
Shell Rg shell_rg	31.02 Å
Envelope Rg envelope_rg	24.01 Å
Shape Rg shape_rg	24.14 Å
Total Rg total_rg	25.02 Å
Total atoms total_atoms	3309
Residues n_residues	442
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.6 Å
Rg (real space) rg_real	25.08 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	3.8450e+07
I(0) uncertainty (real space) i0_real_error	5.7530e+05
Rg (reciprocal space) rg_reciprocal	25.09 Å
I(0) (reciprocal space) i0_reciprocal	38450000.0000
Solution quality estimate total_estimate	0.8995
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.298
Kurtosis Kurtosis kurtosis	-0.462
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7529000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.969

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Light chain of 1080 Fab
Molecular weight formula_weight	23444.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3816

QVLTQTASPVSAAVGNTVTITCQSSQSVWKNNDLSWYQQKLGQPPKLLIYYASTLASGVSSRFKASGSGTQFTLTISDVQCDDAGTYYCVGSYDCSSADCNAFGGGTKVVVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Heavy chain of 1080 Fab
Molecular weight formula_weight	22567.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QSEEESGGRLVTPETPLTLTCTASGIDLSKWPMTWVRQAPGKGLEWIGIIGRSGSTNYASWAKGRFTISKTSTTVDLKMTSPTTEDTATYFCARGGSYYDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Sodium channel protein type 9 subunit alpha
Molecular weight formula_weight	1401.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

EHHPMTEEFKN

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	507

▶

8. Citations (1)

▶

Unit-cell length a length_a	78.965 Å
Unit-cell length b length_b	78.965 Å
Unit-cell length c length_c	147.048 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.620 Å
Low-resolution limit resolution_low	28.650 Å
R factor r_factor	0.1942
R_work r_work	0.1937
R_free r_free	0.2103

fit	/app/data/saxs_computation/yh/8yhz/8yhz.fit
pddf	/app/data/pr_computation/yh/8yhz/8yhz.pr.out
profile	/app/data/saxs_computation/yh/8yhz/8yhz.dat

The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

Sodium channel protein type 9 subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)