SMTL ID : 2p10.1

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9387) FROM MESORHIZOBIUM LOTI MAFF303099 AT 2.15 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

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

ACT.1: 7 residues within 4Å: Chain A: L.71, N.102, P.129, T.130, V.131 Chain E: L.72, A.73 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:A.73, A:N.102, A:N.102 Hydrophobic interactions: A:P.129, A:V.131 ACT.2: 3 residues within 4Å: Chain A: P.173, E.174, V.177 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.174 ACT.3: 3 residues within 4Å: Chain A: S.212, N.215, E.216 No protein-ligand interaction detected (PLIP) ACT.8: 7 residues within 4Å: Chain B: L.71, N.102, T.104, P.129, V.131 Chain D: L.72, A.73 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:P.129, B:V.131 Hydrogen bonds: B:N.102, D:A.73 ACT.9: 8 residues within 4Å: Chain B: Y.55, S.57, R.61, F.128, Y.169, H.190, H.233, A.259 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.128 Hydrogen bonds: B:Y.55, B:Y.169 Water bridges: B:S.260 Salt bridges: B:R.61, B:H.233 ACT.13: 7 residues within 4Å: Chain C: L.71, N.102, T.104, P.129, V.131 Chain F: L.72, A.73 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:P.129, C:V.131 Hydrogen bonds: C:N.102, F:A.73 ACT.14: 5 residues within 4Å: Chain C: R.59, E.87 Chain D: R.59, E.87 Ligands: ACT.15 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:R.59 Water bridges: D:R.59, D:R.59, D:R.59, C:R.59 Salt bridges: D:R.59, C:R.59 ACT.15: 5 residues within 4Å: Chain B: F.107 Chain C: R.86, E.87 Chain D: R.59 Ligands: ACT.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:E.87 Water bridges: C:E.87, D:Y.60 Salt bridges: C:R.86 ACT.16: 7 residues within 4Å: Chain C: Y.55, R.61, F.128, Y.169, H.190, H.233, A.259 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.128 Hydrogen bonds: C:Y.55 Water bridges: C:H.190, C:S.260 Salt bridges: C:R.61, C:H.233 ACT.19: 8 residues within 4Å: Chain B: L.72, A.73, Y.74 Chain D: L.71, N.102, T.104, P.129, V.131 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:A.73, D:N.102, D:N.102 Hydrophobic interactions: D:P.129, D:V.131 ACT.20: 8 residues within 4Å: Chain D: Y.55, S.57, R.61, F.128, Y.169, H.190, H.233, A.259 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.128 Water bridges: D:S.260 Salt bridges: D:R.61, D:H.233 ACT.22: 7 residues within 4Å: Chain A: L.72, A.73 Chain E: L.71, N.102, T.104, P.129, V.131 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:P.129, E:V.131 Hydrogen bonds: E:N.102, A:A.73 ACT.23: 7 residues within 4Å: Chain C: L.72, A.73, Y.74 Chain F: L.71, N.102, T.104, P.129 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:P.129 Hydrogen bonds: F:N.102, C:A.73

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: T.194, H.233, G.258, A.259, S.260, S.261 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: Y.55, R.61 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: T.194, H.233, G.258, A.259, S.260, S.261 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain C: T.194, H.233, G.258, A.259, S.260, S.261 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: G.66, S.67, R.264 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain D: T.194, H.233, G.258, A.259, S.260, S.261 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: N.215, S.249, C.250, Q.251 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.215, A:Q.251 Water bridges: A:N.215, A:G.252 GOL.7: 8 residues within 4Å: Chain A: N.76, N.78, Q.79, D.105, F.107, M.108, F.113 Chain F: R.86 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:R.86, A:N.76, A:Q.79, A:D.105 GOL.11: 5 residues within 4Å: Chain B: R.19, D.48, I.49, H.94, T.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.19, B:H.94, B:H.94 GOL.12: 6 residues within 4Å: Chain B: N.76, F.107, M.108, V.109, F.113 Chain C: R.86 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.76, B:V.109, C:R.86 Water bridges: B:N.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of hypothetical protein (NP_085906.1) from Mesorhizobium loti at 2.15 A resolution. To be published

Release Date

2007-03-20

Peptides

Mll9387 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Mll9387 protein