SMTL ID : 4nhe.2 (1 other biounit)

The crystal structure of oxidoreductase (Gfo/Idh/MocA family) from Streptococcus pneumoniae TIGR4 in complex with NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 23 residues within 4Å: Chain A: G.11, T.12, G.13, I.15, S.36, R.37, T.41, A.72, S.73, P.74, N.75, L.77, H.78, E.95, K.96, P.97, R.124, N.167, F.173, D.180, Y.184, M.280 Ligands: FMT.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.15, A:I.15 Hydrogen bonds: A:T.12, A:T.12, A:T.12, A:R.37, A:R.37, A:S.73, A:N.75, A:E.95, A:K.96, A:R.124, A:N.167 Water bridges: A:G.11, A:G.11, A:G.13, A:S.36, A:R.37, A:R.37, A:K.38, A:N.75 Salt bridges: A:R.37 pi-Cation interactions: A:R.37, A:R.37 NAP.11: 23 residues within 4Å: Chain B: G.11, T.12, G.13, I.15, S.36, R.37, T.41, A.72, S.73, P.74, N.75, L.77, H.78, E.95, K.96, P.97, R.124, N.167, F.173, D.180, Y.184, M.280 Ligands: FMT.12 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.15, B:I.15 Hydrogen bonds: B:T.12, B:T.12, B:T.12, B:R.37, B:R.37, B:S.73, B:N.75, B:E.95, B:K.96, B:R.124, B:N.167 Water bridges: B:G.11, B:G.11, B:G.13, B:S.36, B:R.37, B:R.37, B:K.38, B:N.75 Salt bridges: B:R.37 pi-Cation interactions: B:R.37, B:R.37

12 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: K.96, D.180, L.181, Y.184 Ligands: NAP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.96, A:Y.184 FMT.3: 8 residues within 4Å: Chain A: V.99, S.100, Q.101, P.102, M.179, H.310, L.313, Y.314 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.99 Water bridges: A:R.317 FMT.4: 3 residues within 4Å: Chain A: T.244, D.245, H.264 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.265, A:Q.265 FMT.5: 4 residues within 4Å: Chain A: Y.126, R.191, L.298, W.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.126 Water bridges: A:Y.126, A:H.127 FMT.6: 6 residues within 4Å: Chain A: P.74, N.75, N.167, V.168, F.173, G.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.75 FMT.7: 2 residues within 4Å: Chain A: S.154, K.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.231 Water bridges: A:S.155, A:D.180 FMT.12: 5 residues within 4Å: Chain B: K.96, D.180, L.181, Y.184 Ligands: NAP.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.96, B:Y.184 FMT.13: 8 residues within 4Å: Chain B: V.99, S.100, Q.101, P.102, M.179, H.310, L.313, Y.314 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.99 Water bridges: B:R.317 FMT.14: 3 residues within 4Å: Chain B: T.244, D.245, H.264 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.265, B:Q.265 FMT.15: 4 residues within 4Å: Chain B: Y.126, R.191, L.298, W.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.126 Water bridges: B:Y.126, B:H.127 FMT.16: 6 residues within 4Å: Chain B: P.74, N.75, N.167, V.168, F.173, G.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.75 FMT.17: 2 residues within 4Å: Chain B: S.154, K.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.231 Water bridges: B:S.155, B:D.180

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: N.297, Q.300, T.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.297, A:T.301 Water bridges: A:N.297 GOL.9: 5 residues within 4Å: Chain A: E.113, N.116, C.117, F.118, L.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.113, A:N.116, A:N.116 GOL.18: 3 residues within 4Å: Chain B: N.297, Q.300, T.301 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.297, B:T.301 Water bridges: B:N.297 GOL.19: 5 residues within 4Å: Chain B: E.113, N.116, C.117, F.118, L.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.113, B:N.116, B:N.116

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

ACT.10: 1 residues within 4Å: Chain A: K.135 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.135 ACT.20: 1 residues within 4Å: Chain B: K.135 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The crystal structure of oxidoreductase (Gfo/Idh/MocA family) from Streptococcus pneumoniae TIGR4 in complex with NADP. To be Published

Release Date

2013-11-27

Peptides

Oxidoreductase, Gfo/Idh/MocA family: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Oxidoreductase, Gfo/Idh/MocA family

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