SAXSdb — 6qv1

▼

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

ABC transporter, ATP-binding protein

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

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 A； UniProt 2–577	Fragment：ABC transporter Mutation：D41A	Uncharacterized ABC transporter ATP-binding protein TM_0288 × 1 （Q9WYC4） Nb_TM1 × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.05M Glycine, 0.225M NaCl, 21% (w/v) PEG 550MME	Resolution 3.48 Å R-free 0.303
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 2–577	Fragment：ABC transporter Mutation：D41A	Uncharacterized ABC transporter ATP-binding protein TM_0288 × 1 （Q9WYC4） Nb_TM1 × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.05M Glycine, 0.225M NaCl, 21% (w/v) PEG 550MME	Resolution 3.48 Å R-free 0.303

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 6QV1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QF4 Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation Deposited 2011-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–577（576 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；29% (w/v) polyethylene glycol 400, 50mM Na-cacodylate, 100mM CaCl2, 2.5mM AMP-PNP, 3mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.90 Å R-free 0.263
4Q4A Improved model of AMP-PNP bound TM287/288 Deposited 2014-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–577（576 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293.15 K；29% (w/v) polyethylene glycol 400, 50mM Na-cacodylate, 100mM CaCl2, 2.5mM AMP-PNP, 3mM MgCl2, pH 5.5, VAPOR DIFFUSION, temperature 293.15K	Resolution 2.60 Å R-free 0.268
4Q4H TM287/288 in its apo state Deposited 2014-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–577（576 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；26 % (w/v) polyethylene glycol (PEG) 400, 50 mM Na-cacodylate, 50 mM CaCl2, 2.5 mM ADP and 3 mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.53 Å R-free 0.290
4Q4J Structure of crosslinked TM287/288_S498C_S520C mutant Deposited 2014-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–577（576 aa）	Mutation：C28S, C73S, C496S, S498C, C519S, S520C, C598S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；32 % PEG 400, 50 mM Na-Acetate pH 5 and 500 mM KCl, 2.5 mM AMP-PNP, 3 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.20 Å R-free 0.287
4Q7K Structure of NBD287 of TM287/288 Deposited 2014-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–577（248 aa） Fragment：unp residues 330-577	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；100 mM Tris-HCl, 100 mM sodium acetate, 25 % PEG2000 MME, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.80 Å R-free 0.211
6QUZ Structure of ATPgS-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–577（576 aa） Fragment：ABC transporter	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.035M NaCl, 11.5% (w/v) PEG 6000	Resolution 3.21 Å R-free 0.263
6QUZ Structure of ATPgS-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–577（576 aa） Fragment：ABC transporter	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.035M NaCl, 11.5% (w/v) PEG 6000	Resolution 3.21 Å R-free 0.263
6QV0 Structure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–577（576 aa） Fragment：ABC transporter	Mutation：D41A	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.025M NaCl, 12% (w/v) PEG 6000	Resolution 3.12 Å R-free 0.264
6QV0 Structure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–577（576 aa） Fragment：ABC transporter	Mutation：D41A	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.025M NaCl, 12% (w/v) PEG 6000	Resolution 3.12 Å R-free 0.264
6QV2 Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2 Deposited 2019-03-01	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–577（576 aa） Fragment：ABC transporter	Mutation：D41A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M TRIS, 0.1M NaCl, 30% (v/v) PEG 400	Resolution 4.23 Å R-free 0.330
6QV2 Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2 Deposited 2019-03-01	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–577（576 aa） Fragment：ABC transporter	Mutation：D41A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M TRIS, 0.1M NaCl, 30% (v/v) PEG 400	Resolution 4.23 Å R-free 0.330

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9WYC3_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–587； UniProt 2–577 Author chain C； PDBConstruct 12–587； UniProt 2–577

Uncharacterized ABC transporter ATP-binding protein TM_0288

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

UniProt Q9WYC4

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 B； UniProt 1–598	Fragment：ABC transporter Mutation：D65A, E517A	ABC transporter, ATP-binding protein × 1 （Q9WYC3） Nb_TM1 × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.05M Glycine, 0.225M NaCl, 21% (w/v) PEG 550MME	Resolution 3.48 Å R-free 0.303
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1–598	Fragment：ABC transporter Mutation：D65A, E517A	ABC transporter, ATP-binding protein × 1 （Q9WYC3） Nb_TM1 × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.05M Glycine, 0.225M NaCl, 21% (w/v) PEG 550MME	Resolution 3.48 Å R-free 0.303

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 6QV1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QF4 Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation Deposited 2011-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–598（598 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；29% (w/v) polyethylene glycol 400, 50mM Na-cacodylate, 100mM CaCl2, 2.5mM AMP-PNP, 3mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.90 Å R-free 0.263
4Q4A Improved model of AMP-PNP bound TM287/288 Deposited 2014-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–598（598 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293.15 K；29% (w/v) polyethylene glycol 400, 50mM Na-cacodylate, 100mM CaCl2, 2.5mM AMP-PNP, 3mM MgCl2, pH 5.5, VAPOR DIFFUSION, temperature 293.15K	Resolution 2.60 Å R-free 0.268
4Q4H TM287/288 in its apo state Deposited 2014-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–598（598 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；26 % (w/v) polyethylene glycol (PEG) 400, 50 mM Na-cacodylate, 50 mM CaCl2, 2.5 mM ADP and 3 mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.53 Å R-free 0.290
4Q4J Structure of crosslinked TM287/288_S498C_S520C mutant Deposited 2014-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–598（598 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；32 % PEG 400, 50 mM Na-Acetate pH 5 and 500 mM KCl, 2.5 mM AMP-PNP, 3 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 3.20 Å R-free 0.287
4Q7L Structure of NBD288 of TM287/288 Deposited 2014-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 353–598（246 aa） Fragment：unp residues 353-598	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；100 mM Tris-HAOAc pH 7.5, 200 mM MgCl2, 8 % PEG550 MME, 8 % PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.35 Å R-free 0.236
4Q7L Structure of NBD288 of TM287/288 Deposited 2014-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 353–598（246 aa） Fragment：unp residues 353-598	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；100 mM Tris-HAOAc pH 7.5, 200 mM MgCl2, 8 % PEG550 MME, 8 % PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.35 Å R-free 0.236
4Q7L Structure of NBD288 of TM287/288 Deposited 2014-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 353–598（246 aa） Fragment：unp residues 353-598	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；100 mM Tris-HAOAc pH 7.5, 200 mM MgCl2, 8 % PEG550 MME, 8 % PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.35 Å R-free 0.236
4Q7M Structure of NBD288-Avi of TM287/288 Deposited 2014-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 353–598（246 aa） Fragment：unp residues 353-598	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；100 mM Sodium acetate, 6 % PEG550 MME, 6 % PEG20000, 200 mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.30 Å R-free 0.236
6QUZ Structure of ATPgS-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–598（598 aa） Fragment：ABC transporter	Mutation：E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.035M NaCl, 11.5% (w/v) PEG 6000	Resolution 3.21 Å R-free 0.263
6QUZ Structure of ATPgS-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–598（598 aa） Fragment：ABC transporter	Mutation：E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.035M NaCl, 11.5% (w/v) PEG 6000	Resolution 3.21 Å R-free 0.263
6QV0 Structure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.025M NaCl, 12% (w/v) PEG 6000	Resolution 3.12 Å R-free 0.264
6QV0 Structure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35 Deposited 2019-03-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1M Sodium acetate, 0.025M NaCl, 12% (w/v) PEG 6000	Resolution 3.12 Å R-free 0.264
6QV2 Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2 Deposited 2019-03-01	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M TRIS, 0.1M NaCl, 30% (v/v) PEG 400	Resolution 4.23 Å R-free 0.330
6QV2 Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2 Deposited 2019-03-01	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–598（598 aa） Fragment：ABC transporter	Mutation：D65A, E517A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M TRIS, 0.1M NaCl, 30% (v/v) PEG 400	Resolution 4.23 Å R-free 0.330

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Y288_THEMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–598； UniProt 1–598 Author chain D； PDBConstruct 1–598； UniProt 1–598

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6qv1
Deposition date deposition_date	2019-03-01
Structure title title	Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM1
Keywords keywords	ABC exporter, ABC transporter, Membrane Transporter, MEMBRANE PROTEIN, nanobody; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	57.76 Å
Radius of gyration Rg (electron density) rg_electron	57.65 Å
Forward intensity I(0) i0	1035530000.00
Molecular weight molecular_weight	283130.0 kDa
Excluded volume excluded_volume	360120 Å³
Envelope volume envelope_volume	537410 Å³
Hydration-shell volume shell_volume	76809 Å³
Envelope diameter envelope_diameter	225.8 Å
Shell Rg shell_rg	62.67 Å
Envelope Rg envelope_rg	55.92 Å
Shape Rg shape_rg	57.65 Å
Total Rg total_rg	57.75 Å
Total atoms total_atoms	19916
Residues n_residues	2514
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	200.5 Å
Rg (real space) rg_real	57.92 Å
Rg uncertainty (real space) rg_real_error	2.22 Å
I(0) (real space) i0_real	1.0350e+09
I(0) uncertainty (real space) i0_real_error	2.1710e+07
Rg (reciprocal space) rg_reciprocal	57.59 Å
I(0) (reciprocal space) i0_reciprocal	1035000000.0000
Solution quality estimate total_estimate	0.8196
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	89.1 Å
Skewness Skewness skewness	0.282
Kurtosis Kurtosis kurtosis	-0.441
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	105800000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.671; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.846; Smooth: 0.793

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ABC transporter, ATP-binding protein
Molecular weight formula_weight	65016.8 kDa
Mutation mutation	D41A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	19916

GPSGSGGGGGSKTLARYLKPYWIFAVLAPLFMVVEVICDLSQPTLLARIVAEGIARGDFSLVLKTGILMLIVALIGAVGGIGCTVFASYASQNFGADLRRDLFRKVLSFSISNVNRFHTSSLITRLTNDVTQLQNLVMMLLRIVVRAPLLFVGGIVMAVSINVKLSSVLIFLIPPIVLLFVWLTKKGNPLFRKIQESTDEVNRVVRENLLGVRVVRAFRREEYENENFRKANESLRRSIISAFSLIVFALPLFIFIVNMGMIAVLWFGGVLVRNNQMEIGSIMAYTNYLMQIMFSLMMIGNILNFIVRASASAKRVLEVLNEKPAIEEADNALALPNVEGSVSFENVEFRYFENTDPVLSGVNFSVKPGSLVAVLGETGSGKSTLMNLIPRLIDPERGRVEVDELDVRTVKLKDLRGHISAVPQETVLFSGTIKENLKWGREDATDDEIVEAAKIAQIHDFIISLPEGYDSRVERGGRNFSGGQKQRLSIARALVKKPKVLILDDCTSSVDPITEKRILDGLKRYTKGCTTFIITQKIPTALLADKILVLHEGKVAGFGTHKELLEHCKPYREIYESQFGNGVMNDA

来源 Source

来源生物 organism	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
NCBI Class编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Uncharacterized ABC transporter ATP-binding protein TM_0288
Molecular weight formula_weight	67758.9 kDa
Mutation mutation	D65A, E517A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MPEIRRRPHGPILEKPALKNPTATLRRLLGYLRPHTFTLIMVFVFVTVSSILGVLSPYLIGKTIAVVFVPRRFDLLPRYMLILGTIYALTSLLFWLQGKIMLTLSQDVVFRLRKELFEKLQRVPVGFFDRTPHGDIISRVINDVDNINNVLGNSIIQFFSGIVTLAGAVIMMFRVNVILSLVTLSIVPLTVLITQIVSSQTRKYFYENQRVLGQLNGIIEEDISGLTVIKLFTREEKEMEKFDRVNESLRKVGTKAQIFSGVLPPLMNMVNNLGFALISGFGGWLALKDIITVGTIATFIGYSRQFTRPLNELSNQFNMIQMALASAERIFEILDLEEEKDDPDAVELREVRGEIEFKNVWFSYDKKKPVLKDITFHIKPGQKVALVGPTGSGKTTIVNLLMRFYDVDRGQILVDGIDIRKIKRSSLRSSIGIVLQDTILFSTTVKENLKYGNPGATDEEIKEAAKLTHSDHFIKHLPEGYETVLTDNGEDLSQGQRQLLAITRAFLANPKILILDAATSNVDTKTEKSIQAAMWKLMEGKTSIIIAHRLNTIKNADLIIVLRDGEIVEMGKHDELIQKRGFYYELFTSQYGLVVEKEA

来源 Source

来源生物 organism	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
NCBI Class编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nb_TM1
Molecular weight formula_weight	12566.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

GPSQGQLVESGGGLVQAGGSLTLSCAASVRDISFFAVGWFRQAPGKQRELVAQMTSLRKINYADSVKGRFTISRDDAKNTVSLQMNSLKPEDTAVYYCHASLPGLPYWGQGTPVTVSA

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6qv1A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6qv1B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6qv1C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	6qv1D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

▶

8. Citations (1)

▶

Unit-cell length a length_a	90.750 Å
Unit-cell length b length_b	199.260 Å
Unit-cell length c length_c	113.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.480 Å
Low-resolution limit resolution_low	34.640 Å
R factor r_factor	0.2690
R_work r_work	0.2670
R_free r_free	0.3030

fit	/app/data/saxs_computation/qv/6qv1/6qv1.fit
pddf	/app/data/pr_computation/qv/6qv1/6qv1.pr.out
profile	/app/data/saxs_computation/qv/6qv1/6qv1.dat

Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM1

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

ABC transporter, ATP-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Uncharacterized ABC transporter ATP-binding protein TM_0288

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 (5)

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

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)