9J1R | pdb_00009j1r

Structure of a triple-helix region of human Collagen type II from Trautec

PDB DOI: https://doi.org/10.2210/pdb9J1R/pdb

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

Deposited: 2024-08-05 Released: 2024-08-21
Deposition Author(s): Fan, X., Chu, Y., Zhai, Y., Fu, S., Li, D., Cao, K., Feng, P., Wang, X., Le, H., Tang, D., Zhang, F., Qian, S.
Funding Organization(s): Jiangsu Trautec Medical Technology Co.,Ltd

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.224 (Depositor), 0.230 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of a triple-helix region of human Collagen type II from Trautec

Fan, X., Chu, Y., Zhai, Y., Fu, S., Li, D., Cao, K., Feng, P., Wang, X., Le, H., Tang, D., Zhang, F., Qian, S.

To be published.

Macromolecule Content

Total Structure Weight: 8.72 kDa
Atom Count: 700
Modeled Residue Count: 85
Deposited Residue Count: 90
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triple-helix region of human collagen type II	A, B, C	30	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

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: 1.45 Å
R-Value Free: 0.224 (Depositor), 0.230 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.777	α = 90
b = 14.204	β = 105.826
c = 48.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Jiangsu Trautec Medical Technology Co.,Ltd	China	CQ20230004/CE20235002/CQ20230005

Revision History (Full details and data files)

Version 1.0: 2024-08-21
Type: Initial release

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.