SAXSdb — 7b80

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

Endoplasmic reticulum chaperone BiP

Cricetulus griseus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 28–549	Mutation：T229A, V461F	Protein adenylyltransferase FICD × 1 （Q9BVA6） AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 3 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1 M Tris pH 8.0 25% PEG 400	Resolution 1.87 Å R-free 0.228

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 7B80	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5O4P Crystal structure of AMPylated GRP78 Deposited 2017-05-30	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 28–549（522 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.5M Lithium Sulfate, 0.1M HEPES pH7.5	Resolution 1.86 Å R-free 0.212
5O4P Crystal structure of AMPylated GRP78 Deposited 2017-05-30	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 28–549（522 aa）	Not recorded	SO4 SULFATE ION × 8 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.5M Lithium Sulfate, 0.1M HEPES pH7.5	Resolution 1.86 Å R-free 0.212
6EOB Crystal structure of AMPylated GRP78 in apo form (Crystal form 1) Deposited 2017-10-09	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 28–549（522 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG1000, 0.1M NaKHPO4, PH6.2, 0.1M NaCl	Resolution 2.00 Å R-free 0.280
6EOC Crystal structure of AMPylated GRP78 in apo form (Crystal form 2) Deposited 2017-10-09	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 28–549（522 aa）	Not recorded	SO4 SULFATE ION × 1 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；5% PEG1000, 0.1M Na2HPO4-Citrate, ph4.2, 0.2M LI2SO4	Resolution 1.67 Å R-free 0.249
6EOE Crystal structure of AMPylated GRP78 with nucleotide Deposited 2017-10-09	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 28–549（522 aa）	Not recorded	FLC CITRATE ANION × 1 SO4 SULFATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；5%PEG1000, 0.1M Na2HPO4-Citrate, PH4.2, 0.2M Li2SO4	Resolution 1.71 Å R-free 0.246
6EOF Crystal structure of AMPylated GRP78 in ADP state Deposited 2017-10-09	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 28–549（522 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；293 K；9% PEG1000, 0.1M Na2HPO4-Citrate, ph4.4, 0.2M Li2SO4	Resolution 1.59 Å R-free 0.225
6H9U Crystal structure of the BiP NBD and MANF SAP complex Deposited 2018-08-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–413（386 aa）	Not recorded	MLT D-MALATE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.92 M sodium malonate	Resolution 1.57 Å R-free 0.204
6HA7 Crystal structure of the BiP NBD and MANF complex Deposited 2018-08-07	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 28–413（386 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；7% PEG6000, 0.1 M Tris-HCl pH7.5	Resolution 2.49 Å R-free 0.256
6HA7 Crystal structure of the BiP NBD and MANF complex Deposited 2018-08-07	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 B 28–413（386 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；7% PEG6000, 0.1 M Tris-HCl pH7.5	Resolution 2.49 Å R-free 0.256
6HAB Crystal structure of BiP V461F (apo) Deposited 2018-08-07	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 28–549（522 aa）	Mutation：V461F	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；8% PEG1000, 0.1M Tris-HCl pH8.5	Resolution 2.08 Å R-free 0.271
6ZYH Crystal structure of GRP78 (70kDa heat shock protein 5 / BiP) ATPase domain in complex with ADP and calcium Deposited 2020-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–406（379 aa） Chain B 28–406（379 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；26% PEG6000, 0.2M CaCl2, 0.1MNaOAc Ph5	Resolution 1.88 Å R-free 0.225
7A4U Crystal structure of lid-truncated apo BiP in an oligomeric state Deposited 2020-08-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–549（522 aa）	Mutation：T229A, V461F	GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M BIS-TRIS propane pH 7.5, 0.2 M trisodium citrate dihydrate, 20% PEG 3350	Resolution 1.77 Å R-free 0.217
7A4V Crystal structure of lid-truncated ADP-bound BiP in an oligomeric state Deposited 2020-08-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–549（522 aa）	Mutation：T229A, V461F	ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 4 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.2 M potassium citrate tribasic monohydrate, 20% PEG 3350	Resolution 1.94 Å R-free 0.226
7B7Z DeAMPylation complex of monomeric FICD and AMPylated BiP (state 1) Deposited 2020-12-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–549（522 aa）	Mutation：T229A, V461F	AMP ADENOSINE MONOPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES pH 6.5 10% PEG 4000 0.2 M NaCl	Resolution 1.70 Å R-free 0.221

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

View Construct and Data Evidence

UniProt name	BIP_CRIGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 2–523； UniProt 28–549

Protein adenylyltransferase FICD

Homo sapiens

UniProt Q9BVA6

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 104–445	Not recorded	Endoplasmic reticulum chaperone BiP × 1 （G3I8R9） AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 1 K POTASSIUM ION × 3 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.1 M Tris pH 8.0 25% PEG 400	Resolution 1.87 Å R-free 0.228

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 7B80	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4U04 Structure of a eukaryotic fic domain containing protein Deposited 2014-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain A 102–445（344 aa） Fragment：UNP residues 102-445 Chain B 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	TAR D(-)-TARTARIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；20% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5	Resolution 2.48 Å R-free 0.245
4U07 ATP bound to eukaryotic FIC domain containing protein Deposited 2014-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain A 102–445（344 aa） Fragment：UNP residues 102-445 Chain B 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；20% peg 3350, 200mM Na K tartrate, 100mM Bist-Tris Propane 7.5	Resolution 2.64 Å R-free 0.258
4U0S Structure of Eukaryotic fic domain containing protein with ADP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain A 102–445（344 aa） Chain B 102–445（344 aa）	Mutation：E234G Mutation：E234G	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；20% peg 3350, 200mM Na K tartrate, 100mM Bis-Tris-Propane 7.5	Resolution 2.49 Å R-free 0.245
4U0U Wild type eukaryotic fic domain containing protein with ADP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain A 102–445（344 aa） Fragment：UNP residues 102-445 Chain B 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	PG4 TETRAETHYLENE GLYCOL × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20% PEG 3350, 200mM Na K tartrate, 100mM Bis-Tris-Propane 7.5	Resolution 2.98 Å R-free 0.256
4U0Z Eukaryotic Fic Domain containing protein with bound APCPP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain A 102–445（344 aa） Fragment：UNP residues 102-445 Chain G 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5	Resolution 2.95 Å R-free 0.251
4U0Z Eukaryotic Fic Domain containing protein with bound APCPP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain A 102–445（344 aa） Fragment：UNP residues 102-445 Chain G 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5	Resolution 2.95 Å R-free 0.251
4U0Z Eukaryotic Fic Domain containing protein with bound APCPP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain B 102–445（344 aa） Fragment：UNP residues 102-445 Chain H 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5	Resolution 2.95 Å R-free 0.251
4U0Z Eukaryotic Fic Domain containing protein with bound APCPP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain C 102–445（344 aa） Fragment：UNP residues 102-445 Chain E 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5	Resolution 2.95 Å R-free 0.251
4U0Z Eukaryotic Fic Domain containing protein with bound APCPP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain C 102–445（344 aa） Fragment：UNP residues 102-445 Chain E 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5	Resolution 2.95 Å R-free 0.251
4U0Z Eukaryotic Fic Domain containing protein with bound APCPP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain D 102–445（344 aa） Fragment：UNP residues 102-445 Chain F 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5	Resolution 2.95 Å R-free 0.251
4U0Z Eukaryotic Fic Domain containing protein with bound APCPP Deposited 2014-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain D 102–445（344 aa） Fragment：UNP residues 102-445 Chain F 102–445（344 aa） Fragment：UNP residues 102-445	Not recorded	APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5	Resolution 2.95 Å R-free 0.251
6I7G Crystal structure of dimeric wild type FICD complexed with ATP Deposited 2018-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 104–445（342 aa） Chain B 104–445（342 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 PEG DI(HYDROXYETHYL)ETHER × 1 1PE PENTAETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Tris pH 7.5; 20% PEG 300; 5% PEG8K; 10% Glycerol	Resolution 2.70 Å R-free 0.319
6I7H Crystal structure of dimeric FICD mutant K256S Deposited 2018-11-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 104–445（342 aa）	Mutation：K256S	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5; 0.05 M Magnesium Chloride; 40% Ethanol	Resolution 2.25 Å R-free 0.259
6I7I Crystal structure of dimeric FICD mutant K256A complexed with MgATP Deposited 2018-11-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 104–445（342 aa）	Mutation：K256A	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Bis-Tris pH 6.5; 0.2 M Magnesium Chloride; 25% PEG3350	Resolution 2.33 Å R-free 0.325
6I7J Crystal structure of monomeric FICD mutant L258D Deposited 2018-11-16	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 104–445（342 aa）	Mutation：L258D	SO4 SULFATE ION × 7 1PE PENTAETHYLENE GLYCOL × 3 PG4 TETRAETHYLENE GLYCOL × 5 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5; 2.0 M Ammonium Sulphate	Resolution 2.65 Å R-free 0.283
6I7K Crystal structure of monomeric FICD mutant L258D complexed with MgATP Deposited 2018-11-16	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 104–445（342 aa）	Mutation：L258D	MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 EOH ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.0 M Sodium Chloride; 10% Ethanol	Resolution 2.54 Å R-free 0.252
6I7L Crystal structure of monomeric FICD mutant L258D complexed with MgAMP-PNP Deposited 2018-11-16	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 104–445（342 aa）	Mutation：L258D	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.5 M Sodium Chloride; 10% Ethanol	Resolution 2.32 Å R-free 0.251
6ZMD Crystal structure of HYPE covalently tethered to BiP bound to AMP-PNP Deposited 2020-07-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 102–445（344 aa）	Mutation：T168A, T183A, E234G, L258D, E404C	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 QMK ~{N}-[2-[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1,2,3-triazol-4-yl]ethyl]ethanamide × 1 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M NaCl, 0.1 M Na/K phosphate pH 6.2 and 10% (w/v) PEG 8000	Resolution 2.64 Å R-free 0.235
7B7Z DeAMPylation complex of monomeric FICD and AMPylated BiP (state 1) Deposited 2020-12-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 104–445（342 aa）	Mutation：L258D, H363A	AMP ADENOSINE MONOPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES pH 6.5 10% PEG 4000 0.2 M NaCl	Resolution 1.70 Å R-free 0.221
9YZ5 human FicD bound with farnesyl pyrophosphate Deposited 2025-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 105–433（329 aa） Chain B 105–433（329 aa）	Not recorded	FPP FARNESYL DIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；100 mM Bis-Tris propane (pH 7.5), 200 mM potassium sodium tartrate, and 21% PEG 3350	Resolution 2.58 Å R-free 0.290

14 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FICD_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 2–343； UniProt 104–445

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7b80
Deposition date deposition_date	2020-12-12
Structure title title	DeAMPylation complex of monomeric FICD and AMPylated BiP (state 2)
Keywords keywords	;FICD, Fic, HYPE, BiP, Grp78, AMPylation, deAMPylation, deAMPylase, ER stress, Complex, adenylation, adenylylation, Hsp70, chaperone, transferase, HYDROLASE ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	34.19 Å
Radius of gyration Rg (electron density) rg_electron	33.78 Å
Forward intensity I(0) i0	146078000.00
Molecular weight molecular_weight	97444.0 kDa
Excluded volume excluded_volume	122350 Å³
Envelope volume envelope_volume	158660 Å³
Hydration-shell volume shell_volume	39764 Å³
Envelope diameter envelope_diameter	119.9 Å
Shell Rg shell_rg	39.63 Å
Envelope Rg envelope_rg	33.91 Å
Shape Rg shape_rg	33.78 Å
Total Rg total_rg	34.21 Å
Total atoms total_atoms	6850
Residues n_residues	863
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

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

Maximum dimension Dmax dmax	110.3 Å
Rg (real space) rg_real	34.30 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.4610e+08
I(0) uncertainty (real space) i0_real_error	2.2120e+06
Rg (reciprocal space) rg_reciprocal	34.23 Å
I(0) (reciprocal space) i0_reciprocal	146100000.0000
Solution quality estimate total_estimate	0.8770
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.6 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.462
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31890000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.730

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Endoplasmic reticulum chaperone BiP
Molecular weight formula_weight	57543.0 kDa
EC 编号 ec_number	3.6.4.10
Mutation mutation	T229A, V461F
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	7575

SGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGAFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTKKSQIFSTASDNQPTFTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFA

来源 Source

来源生物 organism	Cricetulus griseus
通用名 common_name	Chinese hamster
NCBI Class编号 ncbi_taxonomy_id	10029
宿主生物 host_organism	Escherichia coli M15

Entity 2 Entity 2 polymer

Description description	Protein adenylyltransferase FICD
Molecular weight formula_weight	39384.0 kDa
EC 编号 ec_number	2.7.7.-,3.1.4.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

SLEARAALNQALEMKRQGKREKAQKLFMHALKMDPDFVDALTEFGIFSEEDKDIIQADYLYTRALTISPYHEKALVNRDRTLPLVEEIDQRYFSIIDSKVKKVMSIPKGNSALRRVMEETYYHHIYHTVAIEGNTLTLSEIRHILETRYAVPGKSDEEQNEVIGMHAAMKYINTTLVSRIGSVTISDVLEIHRRVLGYVDPVEAGRFRTTQVLVGHHIPPHPQDVEKQMQEFVQWLNSEEAMNLHPVEFAALAHYKLVYIAPFIDGNGRTSRLLMNLILMQAGYPPITIRKEQRSDYYHVLEAANEGDVRPFIRFIAKCTETTLDTLLFATTEYSVALPEAQP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	590

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7b80A01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	7b80A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	10 — Fido-like domain

Domain ID domain_id	7b80B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	7b80B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

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8. Citations (1)

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Unit-cell length a length_a	95.000 Å
Unit-cell length b length_b	103.890 Å
Unit-cell length c length_c	104.790 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	52.400 Å
R factor r_factor	0.2021
R_work r_work	0.2008
R_free r_free	0.2278

fit	/app/data/saxs_computation/b8/7b80/7b80.fit
pddf	/app/data/pr_computation/b8/7b80/7b80.pr.out
profile	/app/data/saxs_computation/b8/7b80/7b80.dat

DeAMPylation complex of monomeric FICD and AMPylated BiP (state 2)

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

Endoplasmic reticulum chaperone BiP

State in the Current Structure

Other States of the Same Protein in the Database

Protein adenylyltransferase FICD

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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)