› 5yq5

X-ray diffraction
2.17Å resolution

Crystal structure of human osteomodulin

Released:
DOI: 10.2210/pdb5yq5/pdb
PDB entry 5yq5 coloured by chain, front view.
PDB entry 5yq5 coloured by chain, side view.
PDB entry 5yq5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin.
Tashima T, Nagatoishi S, Caaveiro JMM, Nakakido M, Sagara H, Kusano-Arai O, Iwanari H, Mimuro H, Hamakubo T, Ohnuma SI, Tsumoto K
Commun Biol 1 33 (2018)
PMID: 30271919

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189296 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Osteomodulin Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 430 amino acids
Theoretical weight: 50.16 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q99983 (Residues: 21-421; Coverage: 100%)
Gene names: OMD, SLRR2C, UNQ190/PRO216
Sequence domains: Leucine rich repeat

Ligands and Environments

2 bound ligands:
Ligand NAG 13 x NAG
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21
Unit cell:
a: 75.64Å b: 110.7Å c: 122.15Å
α: 90° β: 106.97° γ: 90°
R-values:
R R work R free
0.218 0.217 0.245
Expression system: Spodoptera frugiperda

Quick links

Citations

1 review citation

Antimicrobial Properties of Extracellular Matrix Scaffolds for Tissue Engineering.
Jiménez-Gastélum et al. (2019)
9 other articles

4 mentions without citation

From Translation to Protein Degradation as Mechanisms for Regulating Biological Functions: A Review on the SLRP Family in Skeletal Tissues.
Zappia et al. (2020)
3 more