MolNFT v1 · #66298 · protein

Crystal structure of allantoinase from bacillus halodurans C-125

3HM7: “Crystal structure of allantoinase from bacillus halodurans C-125”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.77). MolNFT v1 #66298 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3HM7
Type: protein
Length: 2,616 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Allantoinase
EC: 3.5.2.5
UniProt: Q9KAH8
Ligands: ZN
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F	Allantoinase (EC 3.5.2.5)	protein	436	36% helix, 23% strand	Q9KAH8
B	Allantoinase (EC 3.5.2.5)	protein	437	35% helix, 23% strand	Q9KAH8
C	Allantoinase (EC 3.5.2.5)	protein	435	35% helix, 23% strand	Q9KAH8

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	93	0.77	0.98	21	empty
2	88	0.77	0.98	20	empty
3	90	0.76	0.98	22	empty
4	246	0.66	0.83	32	ZN
5	242	0.65	0.83	35	ZN

Interfaces

7 interfaces between chains.

E–F · 970 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 952 Å² buried · 11 hydrogen bonds · protein-protein
B–F · 865 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 822 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 781 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3HM7 · Crystal structure of allantoinase from Bacillus halodurans C-125 · the same entry in another collection · chain F against F, TM-score 1.00
Q9KAH8 · AlphaFold monomer V2.0 prediction for allantoinase (Q9KAH8) · a predicted model of the same protein · chain E 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 Q9KAH8
Elsewhere: RCSB PDB 3HM7 · PDBe 3HM7 · UniProt Q9KAH8

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