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Crystal structure of D-hydantoinase

Analyse Crystal structure of D-hydantoinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1K1D
Type: protein
Length: 3,680 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-hydantoinase
UniProt: Q45515
Ligands: ZN
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	D-hydantoinase	protein	460	34% helix, 23% strand	Q45515

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1145	0.80	0.82	82	empty
2	1131	0.79	0.81	80	empty
3	1183	0.79	0.81	82	empty
4	1184	0.78	0.80	78	empty
5	737	0.74	0.80	95	empty

Interfaces

10 interfaces between chains.

A–B · 1101 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1098 Å² buried · 15 hydrogen bonds · protein-protein
C–F · 1096 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 1068 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 1052 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (carboxylation).

Compared structures

1K1D · Crystal structure of D-hydantoinase · the same entry in another collection · chain H against H, TM-score 1.00
Q45515 · AlphaFold monomer V2.0 prediction for D-hydantoinase (Q45515) · a predicted model of the same protein · 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 Q45515
Elsewhere: RCSB PDB 1K1D · PDBe 1K1D · UniProt Q45515

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