SMTL ID : 3mkv.1

Crystal structure of amidohydrolase eaj56179

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-octamer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.65, H.67, K.193, D.326 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.65, A:H.67, A:D.326 ZN.2: 7 residues within 4Å: Chain A: H.65, K.193, H.234, H.254, D.326 Ligands: ZN.1, SO4.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.234, A:H.254 ZN.5: 5 residues within 4Å: Chain B: H.65, H.67, K.193, D.326 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.65, B:H.67, B:D.326, H2O.10 ZN.6: 5 residues within 4Å: Chain B: K.193, H.234, H.254 Ligands: ZN.5, SO4.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.234, B:H.254, H2O.10 ZN.9: 5 residues within 4Å: Chain C: H.65, H.67, K.193, D.326 Ligands: ZN.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.65, C:H.67, C:D.326 ZN.10: 6 residues within 4Å: Chain C: H.65, K.193, H.234, H.254 Ligands: ZN.9, SO4.11 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.234, C:H.254, H2O.14 ZN.13: 5 residues within 4Å: Chain D: H.65, H.67, K.193, D.326 Ligands: ZN.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.65, D:H.67, D:D.326 ZN.14: 4 residues within 4Å: Chain D: K.193, H.234, H.254 Ligands: ZN.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.234, D:H.254 ZN.18: 5 residues within 4Å: Chain E: H.65, H.67, K.193, D.326 Ligands: ZN.19 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.65, E:H.67, E:D.326 ZN.19: 5 residues within 4Å: Chain E: K.193, H.234, H.254 Ligands: ZN.18, SO4.21 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.234, E:H.254 ZN.22: 5 residues within 4Å: Chain F: H.65, H.67, K.193, D.326 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.65, F:H.67, F:D.326, F:D.326 ZN.23: 7 residues within 4Å: Chain F: H.65, K.193, H.234, H.254, D.326 Ligands: ZN.22, CO3.24 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.234, F:H.254, H2O.25 ZN.25: 5 residues within 4Å: Chain G: H.65, H.67, K.193, D.326 Ligands: ZN.26 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.65, G:H.67, G:D.326 ZN.26: 4 residues within 4Å: Chain G: K.193, H.234, H.254 Ligands: ZN.25 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.234, G:H.254, H2O.28 ZN.29: 5 residues within 4Å: Chain H: H.65, H.67, K.193, D.326 Ligands: ZN.30 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.65, H:H.67, H:D.326, H2O.31 ZN.30: 6 residues within 4Å: Chain H: H.65, K.193, H.234, H.254 Ligands: ZN.29, SO4.31 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.234, H:H.254, H2O.31

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

SO4.3: 9 residues within 4Å: Chain A: H.142, G.199, V.200, A.201, H.234, Y.236, Y.280, D.326 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.200, A:A.201, A:Y.236 Salt bridges: A:H.142, A:H.234, A:H.254 SO4.4: 4 residues within 4Å: Chain A: R.250, G.270, Y.272, K.320 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.272 Salt bridges: A:R.250, A:K.320 SO4.7: 8 residues within 4Å: Chain B: H.142, G.199, V.200, A.201, H.234, Y.236, D.326 Ligands: ZN.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.200, B:A.201 Water bridges: B:H.142 Salt bridges: B:H.142, B:H.234, B:H.254 SO4.8: 4 residues within 4Å: Chain B: R.250, G.270, Y.272, K.320 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.250, B:K.320 SO4.11: 9 residues within 4Å: Chain C: H.142, G.199, V.200, A.201, H.234, Y.236, Y.280, D.326 Ligands: ZN.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.200, C:A.201 Water bridges: C:H.142 Salt bridges: C:H.142, C:H.234 SO4.15: 4 residues within 4Å: Chain D: R.250, G.270, Y.272, K.320 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.272, D:Y.272 Salt bridges: D:R.250, D:K.320 SO4.16: 4 residues within 4Å: Chain D: R.246, L.265, E.268, H.269 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.269 SO4.20: 4 residues within 4Å: Chain E: R.250, G.270, Y.272, K.320 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.270, E:Y.272 Salt bridges: E:R.250, E:K.320 SO4.21: 9 residues within 4Å: Chain E: H.142, G.199, V.200, A.201, H.234, Y.236, H.254, D.326 Ligands: ZN.19 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:V.200, E:A.201, E:Y.236 Salt bridges: E:H.142, E:H.234, E:H.254 SO4.27: 5 residues within 4Å: Chain G: R.250, G.270, Y.272, K.320, E.361 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Y.272 Salt bridges: G:R.250, G:K.320 SO4.31: 8 residues within 4Å: Chain H: H.142, G.199, V.200, A.201, H.234, Y.236, H.254 Ligands: ZN.30 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:V.200, H:A.201 Salt bridges: H:H.142, H:H.234, H:H.254 SO4.32: 5 residues within 4Å: Chain H: R.250, G.270, Y.272, K.320, E.361 2 PLIP interactions: 2 interactions with chain H Salt bridges: H:R.250, H:K.320 SO4.33: 4 residues within 4Å: Chain H: R.246, L.265, E.268, H.269 2 PLIP interactions: 2 interactions with chain H Salt bridges: H:R.246, H:H.269

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain C: L.75, A.143, A.166, L.167, G.168 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.75, C:H.142, C:L.167, C:G.168, C:G.168 GOL.17: 8 residues within 4Å: Chain D: L.75, A.79, A.143, P.145, G.165, A.166, L.167, G.168 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.75, D:L.167, D:G.168, D:G.168

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.24: 8 residues within 4Å: Chain F: H.142, G.199, V.200, A.201, H.234, Y.236, D.326 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.142, F:A.201, F:D.326 Water bridges: F:H.234 CO3.28: 7 residues within 4Å: Chain G: H.142, G.199, V.200, A.201, H.234, Y.236, D.326 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.236, G:Y.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, D.F. et al., Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily . Biochemistry (2010)

Release Date

2010-04-28

Peptides

PUTATIVE AMIDOHYDROLASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

PUTATIVE AMIDOHYDROLASE