SMTL ID : 2fg9.1

CRYSTAL STRUCTURE OF A PUTATIVE 5-NITROIMIDAZOLE ANTIBIOTIC RESISTANCE PROTEIN (BT_3078) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.20 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 8 residues within 4Å: Chain A: H.8, H.10 Chain B: H.8, H.10 Chain C: H.8, H.10 Ligands: NI.4, NI.7 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.8, A:H.10, B:H.8, B:H.10, C:H.8, C:H.10 NI.4: 8 residues within 4Å: Chain A: H.8, H.10 Chain B: H.8, H.10 Chain C: H.8, H.10 Ligands: NI.1, NI.7 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.8, A:H.10, B:H.8, B:H.10, C:H.8, C:H.10 NI.7: 8 residues within 4Å: Chain A: H.8, H.10 Chain B: H.8, H.10 Chain C: H.8, H.10 Ligands: NI.1, NI.4 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.8, A:H.10, B:H.8, B:H.10, C:H.8, C:H.10 NI.10: 8 residues within 4Å: Chain D: H.8, H.10 Chain E: H.8, H.10 Chain F: H.8, H.10 Ligands: NI.13, NI.16 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D, 2 interactions with chain E Metal complexes: F:H.8, F:H.10, D:H.8, D:H.10, E:H.8, E:H.10 NI.13: 8 residues within 4Å: Chain D: H.8, H.10 Chain E: H.8, H.10 Chain F: H.8, H.10 Ligands: NI.10, NI.16 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D, 2 interactions with chain E Metal complexes: F:H.8, F:H.10, D:H.8, D:H.10, E:H.8, E:H.10 NI.16: 8 residues within 4Å: Chain D: H.8, H.10 Chain E: H.8, H.10 Chain F: H.8, H.10 Ligands: NI.10, NI.13 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E Metal complexes: D:H.8, D:H.10, F:H.8, F:H.10, E:H.8, E:H.10

6 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 25 residues within 4Å: Chain A: M.20, T.22, S.91, S.111, E.112, S.113, A.114, M.115, R.117, Q.164, T.166, G.167, K.168, F.170 Chain E: A.40, Y.53, V.55, P.56, M.57, N.58, H.69, S.70, G.75, K.76 Ligands: EDO.3 23 PLIP interactions: 9 interactions with chain A, 14 interactions with chain E Hydrophobic interactions: A:F.170, E:A.40, E:P.56 Hydrogen bonds: A:S.113, A:S.113, A:R.117, A:R.117, A:T.166, E:Y.53, E:P.56, E:N.58, E:H.69, E:H.69, E:G.75, E:K.76, E:K.76 Water bridges: A:T.166, E:H.69, E:G.74, E:G.74 pi-Stacking: A:F.170, A:F.170 Salt bridges: E:K.76 FAD.5: 25 residues within 4Å: Chain B: M.20, T.22, S.91, S.111, E.112, S.113, A.114, M.115, R.117, Q.164, T.166, G.167, K.168, F.170 Chain D: A.40, Y.53, V.55, P.56, M.57, N.58, H.69, S.70, G.75, K.76 Ligands: EDO.6 22 PLIP interactions: 13 interactions with chain D, 9 interactions with chain B Hydrophobic interactions: D:A.40, D:P.56, B:F.170 Hydrogen bonds: D:Y.53, D:P.56, D:N.58, D:H.69, D:G.75, D:K.76, D:K.76, B:S.113, B:S.113, B:R.117, B:R.117, B:T.166 Water bridges: D:H.69, D:G.74, D:G.74, B:T.166 Salt bridges: D:K.76 pi-Stacking: B:F.170, B:F.170 FAD.8: 25 residues within 4Å: Chain C: M.20, T.22, S.91, S.111, E.112, S.113, A.114, M.115, R.117, Q.164, T.166, G.167, K.168, F.170 Chain F: A.40, Y.53, V.55, P.56, M.57, N.58, H.69, S.70, G.75, K.76 Ligands: EDO.9 23 PLIP interactions: 9 interactions with chain C, 14 interactions with chain F Hydrophobic interactions: C:F.170, F:A.40, F:P.56 Hydrogen bonds: C:S.113, C:S.113, C:R.117, C:R.117, C:T.166, F:Y.53, F:P.56, F:N.58, F:H.69, F:H.69, F:G.75, F:K.76, F:K.76 Water bridges: C:T.166, F:H.69, F:G.74, F:G.74 pi-Stacking: C:F.170, C:F.170 Salt bridges: F:K.76 FAD.11: 25 residues within 4Å: Chain B: A.40, Y.53, V.55, P.56, M.57, N.58, H.69, S.70, G.75, K.76 Chain D: M.20, T.22, S.91, S.111, E.112, S.113, A.114, M.115, R.117, Q.164, T.166, G.167, K.168, F.170 Ligands: EDO.12 22 PLIP interactions: 13 interactions with chain B, 9 interactions with chain D Hydrophobic interactions: B:A.40, B:P.56, D:F.170 Hydrogen bonds: B:Y.53, B:P.56, B:N.58, B:H.69, B:G.75, B:K.76, B:K.76, D:S.113, D:S.113, D:R.117, D:R.117, D:T.166 Water bridges: B:H.69, B:G.74, B:G.74, D:T.166 Salt bridges: B:K.76 pi-Stacking: D:F.170, D:F.170 FAD.14: 25 residues within 4Å: Chain A: A.40, Y.53, V.55, P.56, M.57, N.58, H.69, S.70, G.75, K.76 Chain E: M.20, T.22, S.91, S.111, E.112, S.113, A.114, M.115, R.117, Q.164, T.166, G.167, K.168, F.170 Ligands: EDO.15 23 PLIP interactions: 14 interactions with chain A, 9 interactions with chain E Hydrophobic interactions: A:A.40, A:P.56, E:F.170 Hydrogen bonds: A:Y.53, A:P.56, A:N.58, A:H.69, A:H.69, A:G.75, A:K.76, A:K.76, E:S.113, E:S.113, E:R.117, E:R.117, E:T.166 Water bridges: A:H.69, A:G.74, A:G.74, E:T.166 Salt bridges: A:K.76 pi-Stacking: E:F.170, E:F.170 FAD.17: 25 residues within 4Å: Chain C: A.40, Y.53, V.55, P.56, M.57, N.58, H.69, S.70, G.75, K.76 Chain F: M.20, T.22, S.91, S.111, E.112, S.113, A.114, M.115, R.117, Q.164, T.166, G.167, K.168, F.170 Ligands: EDO.18 22 PLIP interactions: 13 interactions with chain C, 9 interactions with chain F Hydrophobic interactions: C:A.40, C:P.56, F:F.170 Hydrogen bonds: C:Y.53, C:P.56, C:N.58, C:H.69, C:G.75, C:K.76, C:K.76, F:S.113, F:S.113, F:R.117, F:R.117, F:T.166 Water bridges: C:H.69, C:G.74, C:G.74, F:T.166 Salt bridges: C:K.76 pi-Stacking: F:F.170, F:F.170

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

EDO.3: 5 residues within 4Å: Chain A: T.22 Chain E: S.70, G.71, K.76 Ligands: FAD.2 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:G.71, E:K.76, A:T.22 EDO.6: 5 residues within 4Å: Chain B: T.22 Chain D: S.70, G.71, K.76 Ligands: FAD.5 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.71, D:K.76, B:T.22 EDO.9: 5 residues within 4Å: Chain C: T.22 Chain F: S.70, G.71, K.76 Ligands: FAD.8 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:G.71, F:K.76, C:T.22 EDO.12: 5 residues within 4Å: Chain B: S.70, G.71, K.76 Chain D: T.22 Ligands: FAD.11 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:T.22, B:G.71, B:K.76 EDO.15: 5 residues within 4Å: Chain A: S.70, G.71, K.76 Chain E: T.22 Ligands: FAD.14 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:T.22, A:G.71, A:K.76 EDO.18: 5 residues within 4Å: Chain C: S.70, G.71, K.76 Chain F: T.22 Ligands: FAD.17 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.71, C:K.76, F:T.22

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of (np_811990.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.20 A resolution. To be published

Release Date

2006-01-10

Peptides

5-nitroimidazole antibiotic resistance protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

5-nitroimidazole antibiotic resistance protein