MolNFT v1 · #15786 · protein

Structure of D-hydantoinase

1NFG: “Structure of D-hydantoinase”. X-ray diffraction, 1 ligand (ZN), 18 pockets (best druggability 0.80). MolNFT v1 #15786 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NFG
Type: protein
Length: 1,828 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-hydantoinase
EC: 3.5.2.2
UniProt: Q8VTT5
Ligands: ZN
Pockets: 18 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	D-hydantoinase (EC 3.5.2.2)	protein	457	33% helix, 25% strand	Q8VTT5

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D

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

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1037	0.80	0.81	67	empty
2	94	0.78	0.98	22	empty
3	672	0.75	0.81	66	empty
4	751	0.75	0.80	68	empty
5	65	0.74	0.99	22	empty

Interfaces

4 interfaces between chains.

C–D · 1340 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1234 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 1112 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1103 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (carboxylation).

Compared structures

1NFG · Structure of D-hydantoinase · the same entry in another collection · chain A against A, TM-score 1.00
Q8VTT5 · AlphaFold monomer V2.0 prediction for D-hydantoinase (Q8VTT5) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8VTT5
Elsewhere: RCSB PDB 1NFG · PDBe 1NFG · UniProt Q8VTT5

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