SMTL ID : 3hzn.4 (6 other biounits)

Structure of the Salmonella typhimurium nfnB dihydropteridine reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

3 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 4 residues within 4Å: Chain A: E.219, V.220 Chain B: S.55 Ligands: SIN.29 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.55, A:E.219 Water bridges: B:K.34, B:S.55, A:E.219 TLA.2: 4 residues within 4Å: Chain A: R.62, E.178, F.179, K.184 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.62, A:E.178, A:K.184 Salt bridges: A:R.62, A:K.184, A:K.184 TLA.22: 10 residues within 4Å: Chain A: F.127 Chain B: K.17, F.73, N.74, K.77, V.165, P.166, I.167, E.168, G.169 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.74, B:N.74, B:K.77, B:P.166, B:E.168, B:G.169 Water bridges: B:K.17 Salt bridges: B:K.17, B:K.77

16 x SIN: SUCCINIC ACID(Non-covalent)

SIN.3: 4 residues within 4Å: Chain A: A.30, S.55, H.83 Chain B: E.219 Ligand excluded by PLIP SIN.4: 5 residues within 4Å: Chain A: A.61, A.64, K.65, E.75, L.79 Ligand excluded by PLIP SIN.5: 12 residues within 4Å: Chain A: R.13, Y.14, S.15, L.154, V.157, A.158, L.162, D.163, A.164, V.165, P.166 Ligands: MLI.15 Ligand excluded by PLIP SIN.6: 6 residues within 4Å: Chain A: A.89, K.90, H.139, T.187, L.189 Ligands: SIN.7 Ligand excluded by PLIP SIN.7: 6 residues within 4Å: Chain A: E.168, S.188, L.189 Chain B: D.137, K.144 Ligands: SIN.6 Ligand excluded by PLIP SIN.8: 5 residues within 4Å: Chain A: E.29, K.32, M.160 Chain B: M.4, D.5 Ligand excluded by PLIP SIN.9: 6 residues within 4Å: Chain A: E.99, V.102, D.103, K.117, A.118, D.121 Ligand excluded by PLIP SIN.10: 4 residues within 4Å: Chain A: T.215 Chain B: W.97, R.100, Y.186 Ligand excluded by PLIP SIN.11: 4 residues within 4Å: Chain A: D.106, A.107, D.108, G.109 Ligand excluded by PLIP SIN.23: 7 residues within 4Å: Chain A: P.41, R.110 Chain B: R.13, Y.14, S.15, K.208, R.210 Ligand excluded by PLIP SIN.24: 6 residues within 4Å: Chain A: M.130 Chain B: Y.71, E.168, F.170, D.171, A.172 Ligand excluded by PLIP SIN.25: 6 residues within 4Å: Chain B: D.5, S.8, V.9, Q.12, A.158 Ligands: MLI.32 Ligand excluded by PLIP SIN.26: 6 residues within 4Å: Chain A: V.220 Chain B: R.62, E.178, F.179, G.180, K.184 Ligand excluded by PLIP SIN.27: 12 residues within 4Å: Chain B: R.13, Y.14, S.15, L.154, V.157, A.158, L.162, D.163, A.164, V.165, P.166 Ligands: MLI.32 Ligand excluded by PLIP SIN.28: 3 residues within 4Å: Chain B: K.17, F.73, K.77 Ligand excluded by PLIP SIN.29: 7 residues within 4Å: Chain A: E.219 Chain B: A.30, K.34, V.53, S.55, H.83 Ligands: TLA.1 Ligand excluded by PLIP

7 x MLI: MALONATE ION(Non-functional Binders)

MLI.12: 10 residues within 4Å: Chain A: R.13, Y.14, S.15, N.203, K.208, R.210 Chain B: P.41, R.110 Ligands: CL.18, CL.35 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Water bridges: B:R.110 Salt bridges: B:R.110, A:R.13, A:K.208, A:K.208, A:R.210 Hydrogen bonds: A:S.15, A:S.15, A:N.203 MLI.13: 4 residues within 4Å: Chain A: M.4, D.5 Chain B: A.3, M.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.5 MLI.14: 8 residues within 4Å: Chain A: F.73, N.74, P.166, I.167, E.168, G.169 Chain B: S.43, F.127 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.167, A:E.168 Hydrogen bonds: A:N.74, A:E.168, A:G.169 MLI.15: 8 residues within 4Å: Chain A: V.9, Q.12, R.13, A.158, G.161, L.162, D.163 Ligands: SIN.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.13 Hydrogen bonds: A:A.158, A:G.161 MLI.30: 7 residues within 4Å: Chain B: A.89, K.90, T.91, H.139, M.142, T.187, L.189 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.89, B:H.139, B:T.187 Water bridges: B:T.187, B:S.188, A:K.144 Salt bridges: B:H.139 MLI.31: 5 residues within 4Å: Chain A: K.34 Chain B: L.213, E.214, L.217, E.219 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:D.31, B:L.213, B:E.219 Salt bridges: A:K.34 Hydrophobic interactions: B:L.217 MLI.32: 8 residues within 4Å: Chain B: Q.12, R.13, A.158, G.161, L.162, D.163 Ligands: SIN.25, SIN.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.12, B:G.161

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

ACT.16: 5 residues within 4Å: Chain A: L.11, Q.12, A.204, L.206, K.208 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.208 ACT.33: 6 residues within 4Å: Chain B: D.176, A.177, G.180, L.181, K.182, E.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.182, B:E.183

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

CL.17: 3 residues within 4Å: Chain A: P.212, L.213 Chain B: Q.38 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain A: K.208, S.209, R.210 Chain B: R.110 Ligands: MLI.12, CL.35 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: R.100 Chain B: L.211, P.212, T.215 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: A.96, W.97, R.100 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain A: Y.39 Chain B: A.10, R.13, K.208 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain B: N.45, E.105, R.110 Ligands: MLI.12, CL.18 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.21: 3 residues within 4Å: Chain A: T.56, E.57, E.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.57, A:E.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, S.M. et al., Structure of the Salmonella typhimurium nfnB dihydropteridine reductase. TO BE PUBLISHED

Release Date

2009-07-07

Peptides

Oxygen-insensitive NAD(P)H nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Oxygen-insensitive NAD(P)H nitroreductase

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