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Osteocalcin from fish argyrosomus regius

Analyse Osteocalcin from fish argyrosomus regius in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VZM
Type: protein
Length: 126 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Osteocalcin
UniProt: Q800Y1
Ligands: MG

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Osteocalcin	protein	43	74% helix, 0% strand	Q800Y1
B	Osteocalcin	protein	42	71% helix, 0% strand	Q800Y1
C	Osteocalcin	protein	41	71% helix, 0% strand	Q800Y1

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

2 interfaces between chains.

A–B · 252 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 228 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified, 2 disulfide (carboxylation, disulfide).

Compared structures

1VZM · Osteocalcin from fish argyrosomus regius · the same entry in another collection · chain A against A, TM-score 1.00
Q800Y1 · AlphaFold monomer V2.0 prediction for osteocalcin (Q800Y1) · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q800Y1
Elsewhere: RCSB PDB 1VZM · PDBe 1VZM · UniProt Q800Y1

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