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Molecular structure of D-hydantoinase from a bacillus sp. AR9: evidence for mercury inhibition

Analyse Molecular structure of D-hydantoinase from a bacillus sp. AR9: evidence for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YNY
Type: protein
Length: 914 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-hydantoinase
EC: 3.5.2.2
UniProt: Q5DLU2
Ligands: MN
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-hydantoinase (EC 3.5.2.2)	protein	455	33% helix, 24% strand	Q5DLU2
B	D-hydantoinase (EC 3.5.2.2)	protein	459	33% helix, 24% strand	Q5DLU2

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 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	353	0.70	0.82	37	MN
2	346	0.70	0.82	38	MN
3	76	0.62	0.90	21	empty
4	75	0.48	0.84	18	empty
5	74	0.47	0.83	18	empty

Compared structures

1YNY · Molecular Structure of D-Hydantoinase from a Bacillus sp. AR9: Evidence for mercury… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q5DLU2
Elsewhere: RCSB PDB 1YNY · PDBe 1YNY · UniProt Q5DLU2

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