SMTL ID : 3kya.1

Crystal structure of Putative phosphatase (NP_812416.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.77 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: R.187, R.189, D.212, Q.248, N.250, Y.266 Ligand excluded by PLIP EDO.2: 8 residues within 4Å: Chain A: A.30, Y.31, S.73, G.74, Y.101, V.106, D.436, E.474 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: Y.31, I.58, V.71, P.72, S.73 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: K.49, V.50, K.51, E.81, I.82, T.83 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: Y.361, R.362, D.363 Ligand excluded by PLIP EDO.6: 1 residues within 4Å: Chain A: E.456 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: P.148, L.149, N.150, K.151 Ligand excluded by PLIP EDO.8: 9 residues within 4Å: Chain A: R.336, D.338, Y.350 Chain B: T.24, P.25, K.33, L.35, Y.68 Ligands: EDO.44 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: L.110, G.112, F.127, D.128, K.134 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: M.105, Y.394, Y.415, Y.451 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: D.147, N.150, H.153, R.228, G.232 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: L.178, N.179, I.180, D.235, D.236, S.238, I.240 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: E.205, R.228, N.229 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: Q.32 Chain B: R.336, Y.350, F.352, P.408 Ligands: EDO.38 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: R.187, R.189, D.212, Q.248, N.250, Y.266 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain B: A.30, Y.31, S.73, G.74, Y.101, V.106, D.436, E.474 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: Y.31, I.58, V.71, P.72, S.73 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: K.49, V.50, K.51, E.81, I.82, T.83 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: Y.361, R.362, D.363 Ligand excluded by PLIP EDO.36: 1 residues within 4Å: Chain B: E.456 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: P.148, L.149, N.150, K.151 Ligand excluded by PLIP EDO.38: 9 residues within 4Å: Chain A: T.24, P.25, K.33, L.35, Y.68 Chain B: R.336, D.338, Y.350 Ligands: EDO.14 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain B: L.110, G.112, F.127, D.128, K.134 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain B: M.105, Y.394, Y.415, Y.451 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain B: D.147, N.150, H.153, R.228, G.232 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain B: L.178, N.179, I.180, D.235, D.236, S.238, I.240 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: E.205, R.228, N.229 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain A: R.336, Y.350, F.352, P.408 Chain B: Q.32 Ligands: EDO.8 Ligand excluded by PLIP

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

ACT.15: 5 residues within 4Å: Chain A: D.340, I.342, K.343 Ligands: ACT.16, ZN.27 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.342, A:K.343 Hydrogen bonds: A:K.343 Water bridges: B:T.65 ACT.16: 8 residues within 4Å: Chain A: D.340, I.342 Chain B: S.21, D.22, Y.37 Ligands: ACT.15, ZN.27, ZN.30 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.22 ACT.17: 4 residues within 4Å: Chain A: W.122, H.161 Ligands: ACT.18, ZN.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.122 Salt bridges: A:H.161 ACT.18: 5 residues within 4Å: Chain A: G.160, H.161, N.186 Ligands: ACT.17, ZN.24 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.162 Salt bridges: A:H.161 ACT.19: 2 residues within 4Å: Chain A: E.102 Chain B: E.409 No protein-ligand interaction detected (PLIP) ACT.45: 5 residues within 4Å: Chain B: D.340, I.342, K.343 Ligands: ACT.46, ZN.57 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.342, B:K.343 Hydrogen bonds: B:K.343 ACT.46: 8 residues within 4Å: Chain A: S.21, D.22, Y.37 Chain B: D.340, I.342 Ligands: ACT.45, ZN.57, ZN.60 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.22 Hydrogen bonds: A:D.22 ACT.47: 4 residues within 4Å: Chain B: W.122, H.161 Ligands: ACT.48, ZN.54 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.122 Salt bridges: B:H.161 ACT.48: 5 residues within 4Å: Chain B: G.160, H.161, N.186 Ligands: ACT.47, ZN.54 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.162 Salt bridges: B:H.161 ACT.49: 2 residues within 4Å: Chain A: E.409 Chain B: E.102 No protein-ligand interaction detected (PLIP)

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

CL.20: 4 residues within 4Å: Chain A: K.47, G.85, E.86, N.89 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain A: N.141, I.329, N.373, C.375, R.398 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain B: K.47, G.85, E.86, N.89 Ligand excluded by PLIP CL.51: 5 residues within 4Å: Chain B: N.141, I.329, N.373, C.375, R.398 Ligand excluded by PLIP

18 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.22: 2 residues within 4Å: Chain A: T.43, D.44 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.44 ZN.23: 2 residues within 4Å: Chain A: H.153, D.168 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.153, A:D.168, H2O.6, H2O.11, H2O.11, H2O.14 ZN.24: 3 residues within 4Å: Chain A: H.161 Ligands: ACT.17, ACT.18 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: A:H.161, H2O.10, ACT.17, ACT.18 ZN.25: 2 residues within 4Å: Chain A: D.364 Ligands: ZN.26 No protein-ligand interaction detected (PLIP) ZN.26: 1 residues within 4Å: Ligands: ZN.25 No protein-ligand interaction detected (PLIP) ZN.27: 3 residues within 4Å: Chain A: D.340 Ligands: ACT.15, ACT.16 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.340, A:D.340, H2O.10, ACT.15 ZN.28: 2 residues within 4Å: Chain A: D.202, E.205 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.205, A:E.205 ZN.29: 1 residues within 4Å: Chain A: E.219 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.219, A:E.219 ZN.30: 2 residues within 4Å: Chain B: D.22 Ligands: ACT.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.22 ZN.52: 2 residues within 4Å: Chain B: T.43, D.44 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.44 ZN.53: 2 residues within 4Å: Chain B: H.153, D.168 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.153, B:D.168, H2O.22, H2O.27, H2O.27, H2O.30 ZN.54: 3 residues within 4Å: Chain B: H.161 Ligands: ACT.47, ACT.48 4 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: B:H.161, H2O.26, ACT.47, ACT.48 ZN.55: 2 residues within 4Å: Chain B: D.364 Ligands: ZN.56 No protein-ligand interaction detected (PLIP) ZN.56: 1 residues within 4Å: Ligands: ZN.55 No protein-ligand interaction detected (PLIP) ZN.57: 3 residues within 4Å: Chain B: D.340 Ligands: ACT.45, ACT.46 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.340, B:D.340, H2O.26, ACT.45 ZN.58: 2 residues within 4Å: Chain B: D.202, E.205 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.205, B:E.205 ZN.59: 1 residues within 4Å: Chain B: E.219 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.219, B:E.219 ZN.60: 2 residues within 4Å: Chain A: D.22 Ligands: ACT.46 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative phosphatase (NP_812416.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.77 A resolution. To be published

Release Date

2009-12-22

Peptides

Putative phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative phosphatase