6Q3P | pdb_00006q3p

Atomic resolution crystal structure of an AAB collagen heterotrimer

PDB DOI: https://doi.org/10.2210/pdb6Q3P/pdb

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

Deposited: 2018-12-04 Released: 2019-12-18
Deposition Author(s): Jalan, A.A., Hartgerink, J.D., Brear, P., Leitinger, B., Farndale, R.W.
Funding Organization(s): Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free:
0.174 (Depositor), 0.177 (DCC)
R-Value Work:
0.143 (Depositor), 0.146 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: in silico
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This is version 1.1 of the entry. See complete history.

Literature

Atomic resolution crystal structure of an AAB collagen heterotrimer

Jalan, A.A., Hartgerink, J.D., Brear, P., Leitinger, B., Farndale, R.W.

(2019) Nat Chem Biol

DOI: https://doi.org/10.1038/s41589-019-0435-y

Macromolecule Content

Total Structure Weight: 13.42 kDa
Atom Count: 1,246
Modeled Residue Count: 148
Deposited Residue Count: 148
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leading Chain of the AAB Collagen Heterotrimer	A	49	Homo sapiens	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Middle Chain of the AAB Collagen Heterotrimer	B	50	Homo sapiens	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Trailing Chain of the AAB Collagen Heterotrimer	C	49	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	A	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO
NLE Query on NLE	A	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free: 0.174 (Depositor), 0.177 (DCC)
R-Value Work: 0.143 (Depositor), 0.146 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 19.736	α = 86.361
b = 28.076	β = 86.681
c = 48.384	γ = 77.21

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Hartgerink, J.D.

Funding Organization	Location	Grant Number
Royal Society	United Kingdom	NF140721

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Refinement description

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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.