SMTL ID : 3ky8.1

Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

4 x UNL: UNKNOWN LIGAND

UNL.1: 5 residues within 4Å: Chain A: F.25, A.27, F.57, Y.86, L.184 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.55, A:T.55, A:Y.86, A:Y.86 Water bridges: A:I.26, A:A.27, A:Q.189 UNL.2: 7 residues within 4Å: Chain A: I.34, N.72, T.73, D.133, G.134, G.135 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.34, A:T.73, A:D.133, A:G.135 UNL.6: 4 residues within 4Å: Chain B: F.25, A.27, T.55, T.153 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.55, B:T.153, B:T.153 Water bridges: B:A.27 UNL.7: 10 residues within 4Å: Chain B: I.34, N.72, T.73, M.76, V.77, Y.86, D.133, G.135, V.163 Ligands: SO4.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.73, B:T.73, B:Y.86, B:D.133, B:G.135

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 9 residues within 4Å: Chain A: G.70, R.71, N.72, T.73, G.134, G.135, V.136, T.137 Ligands: UNL.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.70, A:N.72, A:T.73, A:G.135, A:V.136, A:T.137, A:T.137 Water bridges: A:R.71, A:R.71, A:T.137 SO4.8: 4 residues within 4Å: Chain A: S.171, S.172 Chain B: K.37, R.38 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.37, B:R.38 Hydrogen bonds: A:S.172 Water bridges: A:S.172, A:S.172 SO4.9: 9 residues within 4Å: Chain B: G.70, R.71, N.72, T.73, G.134, G.135, V.136, T.137 Ligands: UNL.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.70, B:N.72, B:N.72, B:T.73, B:V.136, B:T.137, B:T.137 Water bridges: B:R.71, B:R.71 SO4.10: 4 residues within 4Å: Chain B: R.71, S.94, N.95, T.96 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.95, B:N.95, B:T.96 Salt bridges: B:R.71

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: S.172, L.173, S.174, R.194, K.195 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.174, A:S.174, A:R.194, A:R.194, A:K.195 GOL.5: 5 residues within 4Å: Chain A: F.57, M.61, P.85, Y.86, S.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.87 Water bridges: A:S.87, A:S.87 GOL.11: 7 residues within 4Å: Chain B: S.172, L.173, S.174, R.194, K.195, R.196 Ligands: GOL.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.172, B:S.174, B:R.194, B:R.194, B:R.196 GOL.12: 7 residues within 4Å: Chain B: D.145, I.147, D.148, R.194, K.195, R.196 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.145, B:D.148 Water bridges: B:I.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution. To be published

Release Date

2009-12-22

Peptides

Putative riboflavin biosynthesis protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative riboflavin biosynthesis protein