SAXSdb — 5o4p

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

78 kDa glucose-regulated protein

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 28–549	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 28–549	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

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 5O4P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6EOB Crystal structure of AMPylated GRP78 in apo form (Crystal form 1) Deposited 2017-10-09	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 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 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 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 oligomeric state 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 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 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 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 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 28–549（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 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 28–549（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 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 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
7B80 DeAMPylation complex of monomeric FICD and AMPylated BiP (state 2) Deposited 2020-12-12	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 28–549（522 aa）	Mutation：T229A, V461F	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

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G3I8R9_CRIGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–523； UniProt 28–549 Author chain B； PDBConstruct 2–523； UniProt 28–549

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	5o4p
Deposition date deposition_date	2017-05-30
Structure title title	Crystal structure of AMPylated GRP78
Keywords keywords	Bip/GRP78, AMPylation, ATP BINDING PROTEIN; ATP BINDING PROTEIN
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	35.88 Å
Radius of gyration Rg (electron density) rg_electron	35.56 Å
Forward intensity I(0) i0	208518000.00
Molecular weight molecular_weight	114730.0 kDa
Excluded volume excluded_volume	143050 Å³
Envelope volume envelope_volume	185530 Å³
Hydration-shell volume shell_volume	44383 Å³
Envelope diameter envelope_diameter	124.6 Å
Shell Rg shell_rg	41.06 Å
Envelope Rg envelope_rg	35.28 Å
Shape Rg shape_rg	35.57 Å
Total Rg total_rg	35.92 Å
Total atoms total_atoms	8053
Residues n_residues	1040
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	118.5 Å
Rg (real space) rg_real	35.98 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	2.0850e+08
I(0) uncertainty (real space) i0_real_error	3.6030e+06
Rg (reciprocal space) rg_reciprocal	35.92 Å
I(0) (reciprocal space) i0_reciprocal	208500000.0000
Solution quality estimate total_estimate	0.6712
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.0 Å
Skewness Skewness skewness	0.384
Kurtosis Kurtosis kurtosis	-0.471
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51620000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.949; Smooth: 0.851

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	78 kDa glucose-regulated protein
Molecular weight formula_weight	57495.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8750

SGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGAFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVVPTKKSQIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFA

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	13

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	679

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5o4pA01
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	5o4pA02
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	5o4pA03
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

Domain ID domain_id	5o4pA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Substrate Binding Domain Of DNAk; Chain A, domain 1

Domain ID domain_id	5o4pB01
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	5o4pB02
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	5o4pB03
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

Domain ID domain_id	5o4pB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Substrate Binding Domain Of DNAk; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	68.330 Å
Unit-cell length b length_b	118.650 Å
Unit-cell length c length_c	83.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.89 °
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	1.860 Å
Low-resolution limit resolution_low	67.760 Å
R factor r_factor	0.1953
R_work r_work	0.1944
R_free r_free	0.2121

fit	/app/data/saxs_computation/o4/5o4p/5o4p.fit
pddf	/app/data/pr_computation/o4/5o4p/5o4p.pr.out
profile	/app/data/saxs_computation/o4/5o4p/5o4p.dat

Crystal structure of AMPylated GRP78

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

78 kDa glucose-regulated protein

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