6JEC | pdb_00006jec

Structure of a triple-helix region of human collagen type II

PDB DOI: https://doi.org/10.2210/pdb6JEC/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2019-02-05 Released: 2020-02-05
Deposition Author(s): Yang, X., Zhu, Y., Ye, S., Zhang, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.216 (Depositor), 0.214 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Structure of a triple-helix region of human collagen type II.

Yang, X., Zhu, Y., Ye, S., Zhang, R., Lu, L.

To be published.

Macromolecule Content

Total Structure Weight: 8.22 kDa
Atom Count: 700
Modeled Residue Count: 91
Deposited Residue Count: 93
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
human collagen type II	A, B, C	31	Homo sapiens	Mutation(s): 0
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	A, B, C	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.216 (Depositor), 0.214 (DCC)
R-Value Work: 0.179 (Depositor), 0.179 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 19.36	α = 102.76
b = 22.99	β = 92.14
c = 39.909	γ = 113.97

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-02-05
Type: Initial release
Version 1.1: 2025-04-09
Changes: Data collection, Database references, Structure summary

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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.