SMTL ID : 8hfd.1

Crystal structure of allantoinase from E. coli BL21

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 4 residues within 4Å: Chain A: V.212, V.217, R.292, D.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.292 Water bridges: A:V.217 PEG.2: 7 residues within 4Å: Chain A: T.253, Q.257, N.306, E.308 Chain C: Q.257, E.258, G.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.257, A:N.306, A:N.306 PEG.5: 6 residues within 4Å: Chain B: V.212, V.217, E.247, R.292, D.293, N.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.293, B:D.293 Water bridges: B:T.275 PEG.8: 5 residues within 4Å: Chain C: V.212, V.217, R.292, D.293, N.296 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.292 Water bridges: C:V.217, C:E.247 PEG.11: 6 residues within 4Å: Chain D: V.212, V.217, E.247, R.292, D.293, N.296 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.293, D:D.293 Water bridges: D:E.247, D:E.247 PEG.12: 8 residues within 4Å: Chain B: R.256, Q.257, E.258, G.259 Chain D: T.253, Q.257, N.306, E.308 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.257, D:N.306, D:N.306

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.59, H.61, K.146, D.315 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.59, A:H.61, A:D.315 ZN.4: 5 residues within 4Å: Chain A: K.146, F.148, H.186, H.242 Ligands: ZN.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.186, A:H.242 ZN.6: 5 residues within 4Å: Chain B: H.59, H.61, K.146, D.315 Ligands: ZN.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.59, B:H.61, B:D.315 ZN.7: 5 residues within 4Å: Chain B: K.146, F.148, H.186, H.242 Ligands: ZN.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.186, B:H.242 ZN.9: 5 residues within 4Å: Chain C: H.59, H.61, K.146, D.315 Ligands: ZN.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.59, C:H.61, C:D.315 ZN.10: 5 residues within 4Å: Chain C: K.146, F.148, H.186, H.242 Ligands: ZN.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.186, C:H.242 ZN.13: 5 residues within 4Å: Chain D: H.59, K.146, H.186, H.242 Ligands: ZN.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.186, D:H.242 ZN.14: 5 residues within 4Å: Chain D: H.59, H.61, K.146, D.315 Ligands: ZN.13 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.59, D:H.61, D:D.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y.H. et al., Crystal Structure of Allantoinase from Escherichia coli BL21: A Molecular Insight into a Role of the Active Site Loops in Catalysis. Molecules (2023)

Release Date

2023-10-18

Peptides

Allantoinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Allantoinase