SMTL ID : 2r96.1

Crystal structure of E. coli WrbA in complex with FMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: S.10, M.11, Y.12, G.13, H.14, I.15, P.77, T.78, R.79, F.80, S.113, T.114, G.115, T.116, G.117, G.118 Chain B: D.92, H.133 Chain C: Y.143 Ligands: EDO.7, EDO.16 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:M.11, A:Y.12, A:G.13, A:H.14, A:I.15, A:T.78, A:T.78, A:R.79, A:F.80, A:S.113, A:S.113, A:G.115, A:G.117, A:G.118, A:G.118, C:Y.143 Salt bridges: A:H.14 pi-Stacking: A:F.80 FMN.10: 21 residues within 4Å: Chain A: D.92, H.133 Chain B: S.10, M.11, Y.12, G.13, H.14, I.15, P.77, T.78, R.79, F.80, S.113, T.114, G.115, T.116, G.117, G.118 Chain D: Y.143 Ligands: EDO.6, EDO.11 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:M.11, B:Y.12, B:G.13, B:H.14, B:I.15, B:T.78, B:T.78, B:R.79, B:F.80, B:S.113, B:S.113, B:G.117, B:G.118, D:Y.143 Water bridges: B:G.118 Salt bridges: B:H.14 pi-Stacking: B:F.80 FMN.17: 21 residues within 4Å: Chain A: Y.143 Chain C: S.10, M.11, Y.12, G.13, H.14, I.15, P.77, T.78, R.79, F.80, S.113, T.114, G.115, T.116, G.117, G.118 Chain D: D.92, H.133 Ligands: EDO.23, EDO.32 18 PLIP interactions: 1 interactions with chain D, 17 interactions with chain C Hydrogen bonds: D:H.133, C:M.11, C:Y.12, C:G.13, C:H.14, C:I.15, C:T.78, C:T.78, C:R.79, C:F.80, C:S.113, C:S.113, C:G.115, C:G.117, C:G.118, C:G.118 Salt bridges: C:H.14 pi-Stacking: C:F.80 FMN.26: 21 residues within 4Å: Chain B: Y.143 Chain C: D.92, H.133 Chain D: S.10, M.11, Y.12, G.13, H.14, I.15, P.77, T.78, R.79, F.80, S.113, T.114, G.115, T.116, G.117, G.118 Ligands: EDO.22, EDO.27 18 PLIP interactions: 15 interactions with chain D, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:M.11, D:Y.12, D:G.13, D:H.14, D:I.15, D:T.78, D:T.78, D:R.79, D:F.80, D:S.113, D:S.113, D:G.117, D:G.118, C:H.133 Salt bridges: D:H.14 pi-Stacking: D:F.80 Water bridges: B:Y.143, B:Y.143

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

EDO.2: 4 residues within 4Å: Chain A: A.144, A.145, Q.146, E.147 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: T.42, G.85, Q.86 Chain B: T.89, D.92, Q.93 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: Y.188, L.192, K.195 Ligands: EDO.9 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: R.38, E.41, K.54, T.55, Q.56 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: W.98 Ligands: FMN.10, EDO.11 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: G.115, T.116 Chain B: W.98 Chain C: Y.143 Ligands: FMN.1, EDO.16 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: A.23, E.24, S.27, V.34 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: Y.184, E.187, Y.188 Ligands: EDO.4 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: W.98 Chain B: G.115, T.116, G.168 Chain D: Y.143 Ligands: EDO.6, FMN.10 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: K.3, E.33, V.35, D.68, Y.69 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: Y.8, Y.9, S.10, R.38, V.39, E.41, Q.56 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: Y.12, G.13, H.14, T.17, Q.173, P.174 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain B: R.172, Q.173 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: F.80 Chain B: W.98 Ligands: FMN.1, EDO.7 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain C: A.144, A.145, Q.146, E.147 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain C: T.42, G.85, Q.86 Chain D: T.89, D.92, Q.93 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: Y.188, L.192, K.195 Ligands: EDO.25 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain C: R.38, E.41, K.54, T.55, Q.56 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain C: W.98 Ligands: FMN.26, EDO.27 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: Y.143 Chain C: G.115, T.116 Chain D: W.98 Ligands: FMN.17, EDO.32 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: A.23, E.24, S.27, V.34 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: Y.184, E.187, Y.188 Ligands: EDO.20 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: Y.143 Chain C: W.98 Chain D: G.115, T.116, G.168 Ligands: EDO.22, FMN.26 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain D: K.3, E.33, V.35, D.68, Y.69 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain D: Y.8, Y.9, S.10, R.38, V.39, E.41, Q.56 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain D: Y.12, G.13, H.14, T.17, Q.173, P.174 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain D: R.172, Q.173 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: F.80 Chain D: W.98 Ligands: FMN.17, EDO.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wolfova, J. et al., Structural organization of WrbA in apo- and holoprotein crystals. Biochim.Biophys.Acta (2009)

Release Date

2008-09-23

Peptides

Flavoprotein WrbA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

Flavoprotein WrbA

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