SMTL ID : 3s4t.4 (5 other biounits)

Crystal structure of putative amidohydrolase-2 (EFI-target 500288)from Polaromonas sp. JS666

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.174 Chain B: A.137, L.169, S.171 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: R.42, R.45, L.46 Ligands: ACT.5 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: Q.132, L.169 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: F.23, P.62, R.166, N.167 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: R.42, R.45, L.46 Ligands: ACT.10 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain C: F.23, P.62, R.166, N.167 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: R.42, R.45, L.46 Ligands: ACT.21 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: R.247, D.251 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain C: Q.132, L.169 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: R.78, R.115, E.119 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain C: K.323, R.326 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain D: R.42, R.45, L.46 Ligands: ACT.29 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: R.174 Chain D: L.169, S.171 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain D: R.78, R.115 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain D: R.42, R.45 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain D: F.23, P.62, R.166, N.167, F.189 Ligand excluded by PLIP

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 9 residues within 4Å: Chain A: R.35, R.42, L.46, H.50, W.288, N.292, I.293, D.294 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.288 Hydrogen bonds: A:I.293, A:D.294 Salt bridges: A:H.50 ACT.6: 2 residues within 4Å: Chain A: H.295 Chain B: K.238 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:N.292 Salt bridges: A:H.295, B:K.238 ACT.10: 7 residues within 4Å: Chain B: R.42, L.46, W.288, N.292, I.293, D.294 Ligands: SO4.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.288 Hydrogen bonds: B:N.292, B:I.293, B:D.294 Salt bridges: B:H.50 ACT.11: 2 residues within 4Å: Chain B: R.42, R.45 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.45 ACT.21: 9 residues within 4Å: Chain C: R.35, R.42, L.46, H.50, W.288, N.292, I.293, D.294 Ligands: SO4.16 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.288 Hydrogen bonds: C:I.293, C:D.294 Water bridges: C:H.50 Salt bridges: C:H.50 ACT.22: 2 residues within 4Å: Chain C: H.295 Chain D: K.238 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:K.238, C:H.295 Water bridges: C:N.292, C:N.292 ACT.23: 1 residues within 4Å: Chain C: H.232 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.232, C:K.248 ACT.29: 8 residues within 4Å: Chain D: R.35, R.42, L.46, W.288, N.292, I.293, D.294 Ligands: SO4.24 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.46, D:W.288 Hydrogen bonds: D:I.293, D:D.294 Water bridges: D:H.50 Salt bridges: D:H.50

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

EPE.7: 6 residues within 4Å: Chain A: P.25, D.26, K.27 Chain B: T.239, T.240, K.242 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.26, B:T.240, B:T.240, B:T.240, B:K.242 Water bridges: A:K.27 Salt bridges: B:K.242 EPE.8: 6 residues within 4Å: Chain A: T.239, T.240, K.242 Chain B: P.25, D.26, K.27 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.239, A:T.240, A:T.240, B:D.26 Water bridges: B:K.27 EPE.13: 6 residues within 4Å: Chain C: P.25, D.26, K.27 Chain D: T.239, T.240, K.242 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.239, D:T.240, D:T.240, D:T.240, D:K.242, C:D.26 EPE.14: 6 residues within 4Å: Chain C: T.239, T.240, K.242 Chain D: P.25, D.26, K.27 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.239, C:T.240, D:D.26 Salt bridges: C:K.242

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain B: F.23, P.62, R.166, N.167, F.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.167, B:N.167 Water bridges: B:R.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramagopal, U.A. et al., Crystal structure of putative amidohydrolase-2 (EFI-target 500288)from Polaromonas sp. JS666. To be published

Release Date

2011-08-24

Peptides

Amidohydrolase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Amidohydrolase 2

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