SMTL ID : 6c0d.1

Crystal structure of an Amidase (hydantoinase/carbamoylase family) from Burkholderia phymatum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.89, D.100, G.101, H.196 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.89, A:D.100, A:H.196, H2O.3, H2O.12 ZN.12: 4 residues within 4Å: Chain B: H.89, D.100, G.101, H.196 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.89, B:D.100, B:H.196, H2O.22, H2O.31

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

EPE.2: 7 residues within 4Å: Chain A: E.221, R.295, E.330, A.365, S.366 Chain B: H.232, S.282 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.366, B:S.282 Salt bridges: A:E.221, A:E.221, A:R.295, A:E.333, B:H.232 EPE.13: 7 residues within 4Å: Chain A: H.232, S.282 Chain B: E.221, R.295, E.330, A.365, S.366 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.366, A:S.282 Salt bridges: B:E.221, B:E.221, B:R.295, B:E.333, A:H.232

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

SO4.3: 4 residues within 4Å: Chain A: Q.348, A.352, R.411, R.415 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.348, A:R.415, A:R.415 Salt bridges: A:R.411, A:R.415 SO4.4: 5 residues within 4Å: Chain A: Q.344, A.347, Q.348, D.351, W.358 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.344 SO4.14: 4 residues within 4Å: Chain B: Q.348, A.352, R.411, R.415 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Q.348, B:R.415, B:R.415 Salt bridges: B:R.411, B:R.415 SO4.15: 5 residues within 4Å: Chain B: Q.344, A.347, Q.348, D.351, W.358 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.344

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: G.234, T.235 Chain B: R.202, D.266, G.364 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.202, B:R.202, B:D.266 Water bridges: B:A.265, B:D.266 EDO.6: 4 residues within 4Å: Chain A: D.256, W.269 Chain B: M.238, A.246 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.256, A:W.269 EDO.7: 3 residues within 4Å: Chain A: H.320, L.321, V.322 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.321, A:V.322 Water bridges: A:Q.319, A:H.320 EDO.8: 5 residues within 4Å: Chain A: A.373, Q.374, H.375, I.376, P.377 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.374 EDO.9: 6 residues within 4Å: Chain A: L.203, E.204, A.207, K.208, L.209, P.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.208 EDO.10: 3 residues within 4Å: Chain A: D.17, R.20 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.57 EDO.11: 5 residues within 4Å: Chain A: R.20, R.57, D.60, R.113 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.57, A:R.57, A:D.60 EDO.16: 5 residues within 4Å: Chain A: R.202, D.266, G.364 Chain B: G.234, T.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.202, A:R.202 Water bridges: A:A.265, A:D.266 EDO.17: 4 residues within 4Å: Chain A: M.238, A.246 Chain B: D.256, W.269 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.256, B:D.256, B:W.269 EDO.18: 3 residues within 4Å: Chain B: H.320, L.321, V.322 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.320, B:L.321, B:V.322 Water bridges: B:Q.319 EDO.19: 5 residues within 4Å: Chain B: A.373, Q.374, H.375, I.376, P.377 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.374 EDO.20: 6 residues within 4Å: Chain B: L.203, E.204, A.207, K.208, L.209, P.384 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.208 EDO.21: 3 residues within 4Å: Chain B: D.17, R.20 Ligands: EDO.22 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.57 EDO.22: 5 residues within 4Å: Chain B: R.20, R.57, D.60, R.113 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.57, B:R.57, B:D.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of an Amidase (hydantoinase/carbamoylase family) from Burkholderia phymatum. to be published

Release Date

2018-03-21

Peptides

Amidase, hydantoinase/carbamoylase family: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Amidase, hydantoinase/carbamoylase family