8YV3 | pdb_00008yv3

The heterotrimer structure of peptides derived from human collagen type I

PDB DOI: https://doi.org/10.2210/pdb8YV3/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Mutation(s): Yes

Deposited: 2024-03-27 Released: 2025-04-02
Deposition Author(s): Zhu, Y., Yang, X., Sun, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8YV3

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

Literature

The heterotrimer structure of peptides derived from human collagen type I

Zhu, Y., Yang, X., Sun, F.

To be published.

Macromolecule Content

Total Structure Weight: 17.64 kDa
Atom Count: 1,564
Modeled Residue Count: 184
Deposited Residue Count: 186
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-1(I) chain	A, D	31	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P02452 (Homo sapiens) Explore P02452 Go to UniProtKB: P02452
PHAROS: P02452 GTEx: ENSG00000108821
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02452
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen alpha-2(I) chain	B, C, E, F	31	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P08123 (Homo sapiens) Explore P08123 Go to UniProtKB: P08123
PHAROS: P08123 GTEx: ENSG00000164692
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08123
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	B, C, E, F	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.49	α = 82.17
b = 33.043	β = 77.73
c = 38.519	γ = 69.64

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
BALBES	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.