SMTL ID : 4pxy.3 (2 other biounits)

Crystal structure of a Putative thua-like protein (BACUNI_01602) from Bacteroides uniformis ATCC 8492 at 1.50 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

9 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 7 residues within 4Å: Chain A: K.83, D.87, E.90, W.114, P.115, W.116 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.116 Water bridges: A:E.90 Salt bridges: A:D.87, A:E.90 MES.17: 7 residues within 4Å: Chain B: K.83, D.87, E.90, W.114, P.115, W.116 Ligands: EDO.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.116 Water bridges: B:E.90 Salt bridges: B:D.87, B:E.90 MES.33: 7 residues within 4Å: Chain C: K.83, D.87, E.90, W.114, P.115, W.116 Ligands: EDO.46 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.116 Water bridges: C:E.90 Salt bridges: C:D.87, C:E.90 MES.49: 5 residues within 4Å: Chain D: D.87, E.90, W.114, P.115, W.116 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:W.114, D:W.116 Water bridges: D:K.83 Salt bridges: D:D.87, D:E.90 MES.50: 6 residues within 4Å: Chain D: W.131, K.191, D.192 Chain E: Y.11, A.12, G.48 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.191 Water bridges: D:D.192 Salt bridges: D:K.191, D:D.192 pi-Cation interactions: D:W.131 MES.60: 5 residues within 4Å: Chain E: D.87, E.90, W.114, P.115, W.116 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:W.114, E:W.116 Water bridges: E:K.83 Salt bridges: E:D.87, E:E.90 MES.61: 6 residues within 4Å: Chain E: W.131, K.191, D.192 Chain F: Y.11, A.12, G.48 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.191 Water bridges: E:D.192 Salt bridges: E:K.191, E:D.192 pi-Cation interactions: E:W.131 MES.71: 5 residues within 4Å: Chain F: D.87, E.90, W.114, P.115, W.116 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:W.114, F:W.116 Water bridges: F:K.83 Salt bridges: F:D.87, F:E.90 MES.72: 6 residues within 4Å: Chain D: Y.11, A.12, G.48 Chain F: W.131, K.191, D.192 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.191 Water bridges: F:D.192 Salt bridges: F:K.191, F:D.192 pi-Cation interactions: F:W.131

39 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.31, H.103, E.161, H.217 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.31, A:H.103, A:E.161, A:E.161, A:H.217 ZN.3: 1 residues within 4Å: Chain A: H.26 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.26, H2O.3, H2O.11 ZN.4: 2 residues within 4Å: Chain A: E.143 Chain D: E.143 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:E.143, A:E.143, D:E.143, D:E.143, H2O.11 ZN.5: 1 residues within 4Å: Chain A: D.174 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.174, A:D.174, H2O.2, H2O.11 ZN.6: 8 residues within 4Å: Chain A: I.223, D.224 Chain B: I.223, D.224 Chain C: I.223, D.224 Ligands: ZN.22, ZN.38 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:I.223, A:D.224, B:I.223, B:D.224, C:I.223, C:D.224 ZN.7: 1 residues within 4Å: Chain A: E.144 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.144, A:E.144, H2O.12, H2O.12 ZN.8: 2 residues within 4Å: Chain A: K.110, H.113 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.113, H2O.5 ZN.9: 1 residues within 4Å: Chain A: H.113 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.113, H2O.11 ZN.18: 4 residues within 4Å: Chain B: H.31, H.103, E.161, H.217 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.31, B:H.103, B:E.161, B:E.161, B:H.217 ZN.19: 1 residues within 4Å: Chain B: H.26 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.26, H2O.14, H2O.22 ZN.20: 2 residues within 4Å: Chain B: E.143 Chain E: E.143 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: B:E.143, B:E.143, E:E.143, E:E.143, H2O.23 ZN.21: 1 residues within 4Å: Chain B: D.174 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.174, B:D.174, H2O.13, H2O.23 ZN.22: 8 residues within 4Å: Chain A: I.223, D.224 Chain B: I.223, D.224 Chain C: I.223, D.224 Ligands: ZN.6, ZN.38 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Metal complexes: B:I.223, B:D.224, A:I.223, A:D.224, C:I.223, C:D.224 ZN.23: 1 residues within 4Å: Chain B: E.144 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.144, B:E.144, H2O.23, H2O.23 ZN.24: 2 residues within 4Å: Chain B: K.110, H.113 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.113, H2O.16 ZN.25: 1 residues within 4Å: Chain B: H.113 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.113, H2O.23 ZN.34: 4 residues within 4Å: Chain C: H.31, H.103, E.161, H.217 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.31, C:H.103, C:E.161, C:E.161, C:H.217 ZN.35: 1 residues within 4Å: Chain C: H.26 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.26, H2O.25, H2O.33 ZN.36: 2 residues within 4Å: Chain C: E.143 Chain F: E.143 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: C:E.143, C:E.143, F:E.143, F:E.143, H2O.34 ZN.37: 1 residues within 4Å: Chain C: D.174 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.174, C:D.174, H2O.24, H2O.34 ZN.38: 8 residues within 4Å: Chain A: I.223, D.224 Chain B: I.223, D.224 Chain C: I.223, D.224 Ligands: ZN.6, ZN.22 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:I.223, B:D.224, C:I.223, C:D.224, A:I.223, A:D.224 ZN.39: 1 residues within 4Å: Chain C: E.144 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.144, C:E.144, H2O.34, H2O.34 ZN.40: 2 residues within 4Å: Chain C: K.110, H.113 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.113, H2O.27 ZN.41: 1 residues within 4Å: Chain C: H.113 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.113, H2O.34 ZN.51: 4 residues within 4Å: Chain D: H.31, H.103, E.161, H.217 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.31, D:H.103, D:E.161, D:E.161, D:H.217 ZN.52: 1 residues within 4Å: Chain D: H.26 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.26, H2O.38, H2O.43 ZN.53: 8 residues within 4Å: Chain D: I.223, D.224 Chain E: I.223, D.224 Chain F: I.223, D.224 Ligands: ZN.64, ZN.75 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, 2 interactions with chain D Metal complexes: F:I.223, F:D.224, E:I.223, E:D.224, D:I.223, D:D.224 ZN.54: 1 residues within 4Å: Chain D: D.174 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.174, H2O.44, H2O.44, H2O.44 ZN.55: 1 residues within 4Å: Chain D: E.144 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.144, H2O.44 ZN.62: 4 residues within 4Å: Chain E: H.31, H.103, E.161, H.217 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.31, E:H.103, E:E.161, E:E.161, E:H.217 ZN.63: 1 residues within 4Å: Chain E: H.26 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.26, H2O.48, H2O.53 ZN.64: 8 residues within 4Å: Chain D: I.223, D.224 Chain E: I.223, D.224 Chain F: I.223, D.224 Ligands: ZN.53, ZN.75 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E Metal complexes: D:I.223, D:D.224, F:I.223, F:D.224, E:I.223, E:D.224 ZN.65: 1 residues within 4Å: Chain E: D.174 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.174, H2O.54, H2O.54, H2O.54 ZN.66: 1 residues within 4Å: Chain E: E.144 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.144, H2O.54 ZN.73: 4 residues within 4Å: Chain F: H.31, H.103, E.161, H.217 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.31, F:H.103, F:E.161, F:E.161, F:H.217 ZN.74: 1 residues within 4Å: Chain F: H.26 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.26, H2O.58, H2O.63 ZN.75: 8 residues within 4Å: Chain D: I.223, D.224 Chain E: I.223, D.224 Chain F: I.223, D.224 Ligands: ZN.53, ZN.64 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E Metal complexes: D:I.223, D:D.224, F:I.223, F:D.224, E:I.223, E:D.224 ZN.76: 1 residues within 4Å: Chain F: D.174 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.174, H2O.64, H2O.64, H2O.64 ZN.77: 1 residues within 4Å: Chain F: E.144 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.144, H2O.64

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

CL.10: 5 residues within 4Å: Chain A: P.135, P.158, A.159, I.223 Chain C: N.228 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: P.63, Y.64, A.88 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: R.236, W.237 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain A: N.228 Chain B: P.135, P.158, A.159, I.223 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: P.63, Y.64, A.88 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain B: R.236, W.237 Ligand excluded by PLIP CL.42: 5 residues within 4Å: Chain B: N.228 Chain C: P.135, P.158, A.159, I.223 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain C: P.63, Y.64, A.88 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain C: R.236, W.237 Ligand excluded by PLIP CL.56: 6 residues within 4Å: Chain D: P.135, P.158, A.159, I.223 Chain E: G.225, N.228 Ligand excluded by PLIP CL.57: 3 residues within 4Å: Chain D: P.63, Y.64, A.88 Ligand excluded by PLIP CL.58: 2 residues within 4Å: Chain D: R.236, W.237 Ligand excluded by PLIP CL.67: 6 residues within 4Å: Chain E: P.135, P.158, A.159, I.223 Chain F: G.225, N.228 Ligand excluded by PLIP CL.68: 3 residues within 4Å: Chain E: P.63, Y.64, A.88 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain E: R.236, W.237 Ligand excluded by PLIP CL.78: 6 residues within 4Å: Chain D: G.225, N.228 Chain F: P.135, P.158, A.159, I.223 Ligand excluded by PLIP CL.79: 3 residues within 4Å: Chain F: P.63, Y.64, A.88 Ligand excluded by PLIP CL.80: 2 residues within 4Å: Chain F: R.236, W.237 Ligand excluded by PLIP

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

EDO.13: 3 residues within 4Å: Chain A: Y.23, T.39, I.55 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain A: K.83, R.86, D.87, H.113, W.114 Ligands: MES.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.83, A:D.87, A:H.113 Water bridges: A:R.86, A:D.87 EDO.15: 6 residues within 4Å: Chain A: K.68, E.69, Y.70, N.71, D.242, S.244 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.69, A:D.242, A:S.244 Water bridges: A:N.71, A:N.71, A:R.209 EDO.16: 4 residues within 4Å: Chain A: W.131, K.191, D.192 Chain C: G.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.191, A:D.192 EDO.29: 3 residues within 4Å: Chain B: Y.23, T.39, I.55 No protein-ligand interaction detected (PLIP) EDO.30: 6 residues within 4Å: Chain B: K.83, R.86, D.87, H.113, W.114 Ligands: MES.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.83, B:D.87, B:H.113 Water bridges: B:R.86, B:D.87 EDO.31: 6 residues within 4Å: Chain B: K.68, E.69, Y.70, N.71, D.242, S.244 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.69, B:D.242, B:S.244 Water bridges: B:N.71, B:N.71, B:R.209 EDO.32: 4 residues within 4Å: Chain A: G.48 Chain B: W.131, K.191, D.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.191, B:D.192 EDO.45: 3 residues within 4Å: Chain C: Y.23, T.39, I.55 No protein-ligand interaction detected (PLIP) EDO.46: 6 residues within 4Å: Chain C: K.83, R.86, D.87, H.113, W.114 Ligands: MES.33 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.83, C:D.87, C:H.113 Water bridges: C:R.86, C:D.87 EDO.47: 6 residues within 4Å: Chain C: K.68, E.69, Y.70, N.71, D.242, S.244 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.69, C:D.242, C:S.244 Water bridges: C:N.71, C:N.71, C:R.209 EDO.48: 4 residues within 4Å: Chain B: G.48 Chain C: W.131, K.191, D.192 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.191, C:D.192 EDO.59: 5 residues within 4Å: Chain D: K.68, Y.70, N.71, D.242, S.244 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.242, D:S.244 Water bridges: D:R.209 EDO.70: 5 residues within 4Å: Chain E: K.68, Y.70, N.71, D.242, S.244 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.242, E:S.244 Water bridges: E:R.209 EDO.81: 5 residues within 4Å: Chain F: K.68, Y.70, N.71, D.242, S.244 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.242, F:S.244 Water bridges: F:R.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a hypothetical protein (BACUNI_01602) from Bacteroides uniformis ATCC 8492 at 1.50 A resolution. To be published

Release Date

2014-04-23

Peptides

Uncharacterized protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
B

E
B

F
B

Uncharacterized protein

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