SAXSdb — 6h9u

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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 A； UniProt 28–413	Not recorded	Mesencephalic astrocyte-derived neurotrophic factor × 1 （Q9CXI5） 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

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 6H9U	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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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
6HA7 Crystal structure of the BiP NBD and MANF complex Deposited 2018-08-07	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 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 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 28–549（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 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 28–549（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 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 28–549（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 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 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 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 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 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 A； PDBConstruct 1–386； UniProt 28–413

Mesencephalic astrocyte-derived neurotrophic factor

Mus musculus

UniProt Q9CXI5

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 126–169	Not recorded	Endoplasmic reticulum chaperone BiP × 1 （G3I8R9） 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

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 6H9U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6HA7 Crystal structure of the BiP NBD and MANF complex Deposited 2018-08-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 22–179（158 aa）	Not recorded	No recorded non-water small molecule	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 22–179（158 aa）	Not recorded	No recorded non-water small molecule	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

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MANF_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–44； UniProt 126–169

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	6h9u
Deposition date deposition_date	2018-08-06
Structure title title	Crystal structure of the BiP NBD and MANF SAP complex
Keywords keywords	MANF, BiP, NDI, HSP70, ARMET, CHAPERONE; CHAPERONE
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	23.64 Å
Radius of gyration Rg (electron density) rg_electron	22.66 Å
Forward intensity I(0) i0	35869600.00
Molecular weight molecular_weight	46032.0 kDa
Excluded volume excluded_volume	57686 Å³
Envelope volume envelope_volume	70066 Å³
Hydration-shell volume shell_volume	25884 Å³
Envelope diameter envelope_diameter	89.5 Å
Shell Rg shell_rg	29.73 Å
Envelope Rg envelope_rg	23.08 Å
Shape Rg shape_rg	22.67 Å
Total Rg total_rg	23.50 Å
Total atoms total_atoms	3241
Residues n_residues	419
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	86.4 Å
Rg (real space) rg_real	23.60 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	3.5870e+07
I(0) uncertainty (real space) i0_real_error	5.8560e+05
Rg (reciprocal space) rg_reciprocal	23.61 Å
I(0) (reciprocal space) i0_reciprocal	35870000.0000
Solution quality estimate total_estimate	0.8246
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.381
Kurtosis Kurtosis kurtosis	0.030
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13430000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.611; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.963

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Endoplasmic reticulum chaperone BiP
Molecular weight formula_weight	42557.0 kDa
EC 编号 ec_number	3.6.4.10
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3591

GTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGD

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	Mesencephalic astrocyte-derived neurotrophic factor
Molecular weight formula_weight	5212.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TVDLKKLRVKELKKILDDWGEMCKGCAEKSDYIRKINELMPKYA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	House mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	350

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6h9ua1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d6h9ua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	6h9uA01
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	6h9uA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6h9uA03
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	6h9uA04
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	6h9uB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 — SAP domain

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8. Citations (1)

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Unit-cell length a length_a	153.310 Å
Unit-cell length b length_b	66.750 Å
Unit-cell length c length_c	44.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	42.470 Å
R factor r_factor	0.1854
R_work r_work	0.1845
R_free r_free	0.2041

fit	/app/data/saxs_computation/h9/6h9u/6h9u.fit
pddf	/app/data/pr_computation/h9/6h9u/6h9u.pr.out
profile	/app/data/saxs_computation/h9/6h9u/6h9u.dat

Crystal structure of the BiP NBD and MANF SAP complex

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

Mesencephalic astrocyte-derived neurotrophic factor

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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)