SMTL ID : 1gkp.2 (1 other biounit)

D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group C2221

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: K.149, H.182, H.238, S.287 Ligands: ZN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.182, A:H.238, H2O.26, H2O.26 ZN.2: 5 residues within 4Å: Chain A: H.58, H.60, K.149, D.314 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.58, A:H.60, A:D.314, H2O.26 ZN.5: 4 residues within 4Å: Chain B: K.149, H.182, H.238 Ligands: ZN.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.182, B:H.238, H2O.47, H2O.47 ZN.6: 5 residues within 4Å: Chain B: H.58, H.60, K.149, D.314 Ligands: ZN.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.58, B:H.60, B:D.314, H2O.47 ZN.9: 5 residues within 4Å: Chain C: K.149, H.182, H.238, S.287 Ligands: ZN.10 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.182, C:H.238, H2O.74, H2O.74 ZN.10: 5 residues within 4Å: Chain C: H.58, H.60, K.149, D.314 Ligands: ZN.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.58, C:H.60, C:D.314, H2O.74 ZN.14: 5 residues within 4Å: Chain D: K.149, H.182, H.238, S.287 Ligands: ZN.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.182, D:H.238, H2O.97, H2O.97 ZN.15: 5 residues within 4Å: Chain D: H.58, H.60, K.149, D.314 Ligands: ZN.14 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.58, D:H.60, D:D.314, H2O.97

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: K.369, K.372 Chain B: H.360, R.361 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Water bridges: B:D.358, A:D.364, A:K.369, A:K.369, A:K.369 Salt bridges: B:R.361, A:K.369, A:K.372 SO4.4: 2 residues within 4Å: Chain A: Q.106, K.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.106 Water bridges: A:K.109 Salt bridges: A:K.109 SO4.7: 4 residues within 4Å: Chain A: H.360, R.361 Chain B: K.369, K.372 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Water bridges: B:D.364, B:K.369, B:K.369, B:K.369, B:K.369, A:D.358, A:D.358 Salt bridges: B:K.369, B:K.372 SO4.11: 4 residues within 4Å: Chain C: K.369, K.372 Chain D: H.360, R.361 6 PLIP interactions: 6 interactions with chain C Water bridges: C:K.369, C:K.369, C:K.369, C:K.369 Salt bridges: C:K.369, C:K.372 SO4.12: 2 residues within 4Å: Chain C: Q.106, K.109 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.106 Water bridges: C:K.109 Salt bridges: C:K.109 SO4.13: 2 residues within 4Å: Chain C: R.437, V.442 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.437 SO4.16: 4 residues within 4Å: Chain C: H.360, R.361 Chain D: K.369, K.372 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Water bridges: D:K.369, D:K.369, D:K.369, D:K.372, C:D.358, C:R.361 Salt bridges: D:K.369, D:K.372

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 5 residues within 4Å: Chain B: I.43, S.426, V.427, R.437, D.438 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.438 Water bridges: B:D.44, B:K.48, B:K.48 Salt bridges: B:D.438 EPE.17: 5 residues within 4Å: Chain D: I.43, S.426, V.427, R.437, D.438 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.438 Water bridges: D:D.44, D:K.48, D:R.437 Salt bridges: D:K.48, D:D.438

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., X-Ray Structure of a Dihydropyrimidinase from Thermus Sp. At 1.3 A Resolution. J.Mol.Biol. (2002)

Release Date

2002-06-27

Peptides

HYDANTOINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

HYDANTOINASE

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