9X02 | pdb_00009x02

Crystal structure of human type VII collagen vWFA2 domain in complex with homo-trimeric collagen model peptide.

PDB DOI: https://doi.org/10.2210/pdb9X02/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-29 Released: 2026-10-07
Deposition Author(s): Hashimoto, M., Oki, H., Kawahara, K., Fujii, K., Koide, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.217 (Depositor), 0.216 (DCC)
R-Value Work:
0.176 (Depositor), 0.175 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human type VII collagen vWFA2 domain in complex with homo-trimeric collagen model peptide.

Hashimoto, M., Oki, H., Kawahara, K., Fujii, K., Koide, T.

To be published.

Macromolecule Content

Total Structure Weight: 53.27 kDa
Atom Count: 4,361
Modeled Residue Count: 502
Deposited Residue Count: 520
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(VII) chain	A, E	194	Homo sapiens	Mutation(s): 0 Gene Names: COL7A1
UniProt & NIH Common Fund Data Resources
Find proteins for Q02388 (Homo sapiens) Explore Q02388 Go to UniProtKB: Q02388
PHAROS: Q02388 GTEx: ENSG00000114270
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02388
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen model peptide, Short-XGWXGA	B, C, D, F, G B, C, D, F, G, H	22	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth E] SDF format, chain I [auth A] MOL2 format, chain J [auth E] MOL2 format, chain I [auth A] mmCIF format, chain J [auth E] mmCIF format, chain I [auth A]	I [auth A], J [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth E] Interactions & Density Focus chain I [auth A] Focus chain J [auth E]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	B, C, D, F, G B, C, D, F, G, H	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO
KLF Query on KLF	B, C, D, F, G B, C, D, F, G, H	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₂		PRO
NLE Query on NLE	B, C, D, F, G B, C, D, F, G, H	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.217 (Depositor), 0.216 (DCC)
R-Value Work: 0.176 (Depositor), 0.175 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.007	α = 90
b = 37.17	β = 115.77
c = 80.492	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release