MolNFT v1 · #127453 · protein

Crystal structure of human fibromodulin

5MX0: “Crystal structure of human fibromodulin”. X-ray diffraction, 5 ligands (NAG, BMA, FUC), 2 pockets (best druggability 0.72). MolNFT v1 #127453 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MX0
Type: protein
Length: 610 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibromodulin
UniProt: Q06828
Ligands: NAG, BMA, FUC, NI, CL
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibromodulin	protein	304	5% helix, 14% strand	Q06828
B	Fibromodulin	protein	306	6% helix, 14% strand	Q06828

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 8 copies
FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, B
NI · Nickel (II) ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	620	0.72	0.80	71	empty
2	68	0.31	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 368 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

5MX0 · Crystal structure of human fibromodulin · the same entry in another collection · chain A against A, TM-score 1.00
Q06828 · AlphaFold monomer V2.0 prediction for fibromodulin (Q06828) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 Q06828
Elsewhere: RCSB PDB 5MX0 · PDBe 5MX0 · UniProt Q06828

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