MolNFT v1 · #121138 · protein

Crystal structure of triazine hydrolase variant (Y215H/E241Q)

5HMD: “Crystal structure of triazine hydrolase variant (Y215H/E241Q)”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.79). MolNFT v1 #121138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HMD
Type: protein
Length: 911 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Triazine hydrolase
EC: 3.8.1.8
UniProt: Q6SJY7
Ligands: ZN
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Triazine hydrolase (EC 3.8.1.8)	protein	456	39% helix, 23% strand	Q6SJY7
B	Triazine hydrolase (EC 3.8.1.8)	protein	455	39% helix, 22% strand	Q6SJY7

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	136	0.79	0.98	34	empty
2	116	0.77	0.96	28	empty
3	336	0.76	0.86	48	ZN
4	372	0.65	0.79	39	empty
5	87	0.40	0.77	20	empty

Interfaces

1 interface between chains.

A–B · 2729 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

5HMD · Crystal structure of triazine hydrolase variant (Y215H/E241Q) · 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 Q6SJY7
Elsewhere: RCSB PDB 5HMD · PDBe 5HMD · UniProt Q6SJY7

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