SMTL ID : 4i6v.1

The crystal structure of an amidohydrolase 2 from Planctomyces limnophilus DSM 3776

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.28, H.30, D.377 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.28, A:H.30, A:D.377, H2O.96, H2O.97 ZN.6: 3 residues within 4Å: Chain B: H.28, H.30, D.377 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.28, B:H.30, B:D.377, H2O.192, H2O.194 ZN.11: 3 residues within 4Å: Chain C: H.28, H.30, D.377 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.28, C:H.30, C:D.377, H2O.391

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: D.168, F.172, H.173, S.219, P.221, R.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.168, A:D.168, A:R.282 GOL.3: 5 residues within 4Å: Chain A: Y.47, H.48, Y.49, W.347, D.377 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.47, A:Y.49 Water bridges: A:W.346, A:W.347, A:W.347, A:D.377 GOL.7: 5 residues within 4Å: Chain B: D.168, F.172, H.173, S.219, R.282 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.168, B:R.282 Water bridges: B:R.282 GOL.8: 3 residues within 4Å: Chain B: R.314, K.316, P.338 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.58 GOL.9: 9 residues within 4Å: Chain B: L.170, V.171, F.172, H.173, L.174, Q.175, S.252, L.255, S.256 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.170, B:L.174, B:Q.175, B:S.252, B:S.256 GOL.10: 5 residues within 4Å: Chain B: A.83, H.84 Chain C: R.368, N.369, Q.420 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.420, B:H.84 GOL.12: 3 residues within 4Å: Chain C: K.123, S.126, A.127 No protein-ligand interaction detected (PLIP) GOL.13: 4 residues within 4Å: Chain C: D.20, E.21, R.100, Q.139 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.100, C:R.100, C:Q.139 GOL.14: 5 residues within 4Å: Chain C: Y.47, H.48, Y.49, W.347, D.377 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.49, C:W.346 GOL.15: 5 residues within 4Å: Chain A: R.368, N.369, Q.420 Chain C: A.83, H.84 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.420, C:A.83, C:H.84

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

ACT.4: 5 residues within 4Å: Chain A: I.89, K.92 Chain B: E.364, G.406, R.407 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:K.92 Salt bridges: A:K.92, B:R.407 Hydrogen bonds: B:G.406 ACT.5: 6 residues within 4Å: Chain A: K.92, I.95, D.107 Chain B: R.407, W.409, R.413 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.413 Hydrophobic interactions: A:I.95 Hydrogen bonds: A:D.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, Y. et al., The crystal structure of an amidohydrolase 2 from Planctomyces limnophilus DSM 3776. To be Published

Release Date

2013-02-06

Peptides

Amidohydrolase 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Amidohydrolase 2