MolNFT v1 · #129213 · protein

Crystal structure of the oleate hydratase of rhodococcus erythropolis

5ODO · Isomerase: “Crystal structure of the oleate hydratase of rhodococcus erythropolis”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.79). MolNFT v1 #129213 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5ODO
Type: protein
Length: 1,057 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isomerase
Ligands: MG
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isomerase	protein	528	36% helix, 17% strand	—
B	Isomerase	protein	529	36% helix, 17% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B
FMT · Formic acid · additive · 14 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	981	0.79	0.81	102	FMT
2	686	0.76	0.82	67	empty
3	70	0.76	0.99	18	FMT
4	679	0.75	0.81	64	FMT
5	64	0.74	0.98	18	empty

Interfaces

1 interface between chains.

A–B · 746 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5ODO · Crystal Structure of the Oleate hydratase of Rhodococcus erythropolis · the same entry in another collection · chain A 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
Elsewhere: RCSB PDB 5ODO · PDBe 5ODO

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