SMTL ID : 3hzn.3 (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

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

TLA.1: 5 residues within 4Å: Chain A: A.30, K.34, S.55, H.83 Chain B: E.219 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.34, A:S.55, A:S.55 Salt bridges: A:K.34, A:H.83 TLA.14: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.74, B:N.74, B:E.168, B:G.169 Salt bridges: B:K.17, B:K.77

9 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 6 residues within 4Å: Chain A: Q.140, A.143, K.144 Chain B: Q.140, A.143, K.144 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.140, A:Q.140 Salt bridges: B:K.144, A:K.144 Hydrogen bonds: A:Q.140, A:Q.140, A:K.144 SIN.3: 3 residues within 4Å: Chain A: R.62, F.179, K.184 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.184 Salt bridges: A:R.62, A:K.184, A:K.184 SIN.4: 6 residues within 4Å: Chain A: R.100, D.103, Q.104 Chain B: L.211, P.212, T.215 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.100, B:L.211 Hydrogen bonds: A:Q.104 Salt bridges: A:R.100 SIN.5: 3 residues within 4Å: Chain A: T.72, F.73, R.76 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.72 Salt bridges: A:R.76 SIN.6: 6 residues within 4Å: Chain A: D.106, F.111, A.112, T.113, P.114, K.117 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.114 SIN.7: 4 residues within 4Å: Chain A: T.35, Q.38 Chain B: L.213 Ligands: FLC.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.35, A:Q.38, A:Y.39, A:Y.39 SIN.15: 5 residues within 4Å: Chain A: V.220 Chain B: R.62, E.178, F.179, K.184 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.179 Salt bridges: B:R.62, B:K.184, B:K.184 SIN.16: 3 residues within 4Å: Chain B: A.204, L.206 Ligands: MLI.19 No protein-ligand interaction detected (PLIP) SIN.17: 11 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 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:R.13, B:L.154, B:A.158, B:A.164 Hydrogen bonds: B:Y.14, B:A.164 Water bridges: B:T.16 Salt bridges: B:R.13

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

MLI.8: 5 residues within 4Å: Chain A: F.19, R.76, D.80, S.198, E.200 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.80, A:S.198, A:E.200, A:E.200 Water bridges: A:F.19, A:R.76 MLI.9: 9 residues within 4Å: Chain A: F.73, N.74, K.77, V.165, P.166, I.167, E.168, G.169 Chain B: F.127 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.74, A:N.74, A:P.166, A:E.168, A:G.169 Salt bridges: A:K.17, A:K.77 MLI.10: 7 residues within 4Å: Chain A: R.13, Y.14, S.15, N.203, K.208, R.210 Chain B: R.110 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.15, A:S.15, A:N.203 Salt bridges: A:R.13, A:K.208, A:K.208, A:R.210, B:R.110 Water bridges: B:S.42, B:R.110 MLI.11: 6 residues within 4Å: Chain A: L.11, Q.12, R.13, A.204, L.206, K.208 No protein-ligand interaction detected (PLIP) MLI.18: 6 residues within 4Å: Chain A: R.110 Chain B: R.13, Y.14, S.15, K.208, R.210 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.15, B:S.15 Water bridges: B:S.15, B:R.210, B:R.210, A:R.110, A:R.110, A:R.110, A:R.110 Salt bridges: B:R.13, B:K.208, B:K.208, B:R.210, A:R.110 MLI.19: 2 residues within 4Å: Chain B: G.205 Ligands: SIN.16 No protein-ligand interaction detected (PLIP) MLI.20: 7 residues within 4Å: Chain A: K.32, M.160 Chain B: M.4, D.5, I.6, V.7, S.8 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.32, A:K.32 Hydrogen bonds: B:D.5, B:D.5, B:V.7, B:S.8

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

CL.12: 5 residues within 4Å: Chain A: R.13, Y.14, L.154, A.164, V.165 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: A.30, H.83 Ligand excluded by PLIP

1 x FLC: CITRATE ANION(Non-covalent)

FLC.13: 5 residues within 4Å: Chain A: Q.38 Chain B: P.212, L.213, E.214 Ligands: SIN.7 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.212 Hydrogen bonds: B:L.213, B:E.214, A:Q.38, A:Q.38, A:Y.39

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

NA.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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
A

B
B

Oxygen-insensitive NAD(P)H nitroreductase

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