MolNFT v1 · #137391 · protein

Crystal structure of taurine dioxygenase from burkholderia ambifaria

5VN6: “Crystal structure of taurine dioxygenase from burkholderia ambifaria”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.67). MolNFT v1 #137391 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VN6
Type: protein
Length: 541 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Taurine dioxygenase
EC: 1.14.11.17
UniProt: B1YQF4
Ligands: MG
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Taurine dioxygenase (EC 1.14.11.17)	protein	273	27% helix, 26% strand	B1YQF4
B	Taurine dioxygenase (EC 1.14.11.17)	protein	268	27% helix, 26% strand	B1YQF4

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	509	0.67	0.78	46	MG
2	452	0.63	0.77	44	MG
3	275	0.60	0.79	23	empty
4	102	0.31	0.71	19	empty
5	69	0.29	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 938 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5VN6 · Crystal structure of Taurine dioxygenase from Burkholderia ambifaria · 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
Every structure of UniProt B1YQF4
Elsewhere: RCSB PDB 5VN6 · PDBe 5VN6 · UniProt B1YQF4

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