SMTL ID : 3hzn.1 (6 other biounits)

Structure of the Salmonella typhimurium nfnB dihydropteridine reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-octamer

Ligands

44 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 8 residues within 4Å: Chain A: R.13, Y.14, S.15, N.203, K.208, R.210 Chain B: P.41, R.110 Ligand excluded by PLIP SIN.2: 3 residues within 4Å: Chain A: A.30, S.55, H.83 Ligand excluded by PLIP SIN.3: 3 residues within 4Å: Chain A: Q.12, A.204, L.206 Ligand excluded by PLIP SIN.4: 5 residues within 4Å: Chain A: R.62, F.179, G.180, K.184 Chain B: V.220 Ligand excluded by PLIP SIN.5: 5 residues within 4Å: Chain A: Q.140, K.144 Chain B: Q.140, A.143, L.189 Ligand excluded by PLIP SIN.12: 4 residues within 4Å: Chain A: E.219 Chain B: A.30, S.55, H.83 Ligand excluded by PLIP SIN.13: 5 residues within 4Å: Chain A: V.220 Chain B: R.62, F.179, K.184 Ligands: SIN.14 Ligand excluded by PLIP SIN.14: 3 residues within 4Å: Chain B: R.62, E.178 Ligands: SIN.13 Ligand excluded by PLIP SIN.15: 6 residues within 4Å: Chain A: M.130 Chain B: Y.71, F.170, D.171, A.172, E.173 Ligand excluded by PLIP SIN.19: 6 residues within 4Å: Chain C: Q.140, A.143, K.144 Chain D: Q.140, A.143, K.144 Ligand excluded by PLIP SIN.20: 3 residues within 4Å: Chain C: R.62, F.179, K.184 Ligand excluded by PLIP SIN.21: 6 residues within 4Å: Chain C: R.100, D.103, Q.104 Chain D: L.211, P.212, T.215 Ligand excluded by PLIP SIN.22: 8 residues within 4Å: Chain C: T.72, F.73, R.76 Chain E: D.20, K.23, H.197, S.198, V.199 Ligand excluded by PLIP SIN.23: 6 residues within 4Å: Chain C: D.106, F.111, A.112, T.113, P.114, K.117 Ligand excluded by PLIP SIN.24: 4 residues within 4Å: Chain C: T.35, Q.38 Chain D: L.213 Ligands: FLC.30 Ligand excluded by PLIP SIN.32: 5 residues within 4Å: Chain C: V.220 Chain D: R.62, E.178, F.179, K.184 Ligand excluded by PLIP SIN.33: 3 residues within 4Å: Chain D: A.204, L.206 Ligands: MLI.36 Ligand excluded by PLIP SIN.34: 11 residues within 4Å: Chain D: R.13, Y.14, S.15, L.154, V.157, A.158, L.162, D.163, A.164, V.165, P.166 Ligand excluded by PLIP SIN.42: 4 residues within 4Å: Chain E: A.30, S.55, H.83 Chain F: E.219 Ligand excluded by PLIP SIN.43: 5 residues within 4Å: Chain E: A.61, A.64, K.65, E.75, L.79 Ligand excluded by PLIP SIN.44: 12 residues within 4Å: Chain E: R.13, Y.14, S.15, L.154, V.157, A.158, L.162, D.163, A.164, V.165, P.166 Ligands: MLI.54 Ligand excluded by PLIP SIN.45: 6 residues within 4Å: Chain E: A.89, K.90, H.139, T.187, L.189 Ligands: SIN.46 Ligand excluded by PLIP SIN.46: 6 residues within 4Å: Chain E: E.168, S.188, L.189 Chain F: D.137, K.144 Ligands: SIN.45 Ligand excluded by PLIP SIN.47: 5 residues within 4Å: Chain E: E.29, K.32, M.160 Chain F: M.4, D.5 Ligand excluded by PLIP SIN.48: 6 residues within 4Å: Chain E: E.99, V.102, D.103, K.117, A.118, D.121 Ligand excluded by PLIP SIN.49: 4 residues within 4Å: Chain E: T.215 Chain F: W.97, R.100, Y.186 Ligand excluded by PLIP SIN.50: 4 residues within 4Å: Chain E: D.106, A.107, D.108, G.109 Ligand excluded by PLIP SIN.62: 7 residues within 4Å: Chain E: P.41, R.110 Chain F: R.13, Y.14, S.15, K.208, R.210 Ligand excluded by PLIP SIN.63: 6 residues within 4Å: Chain E: M.130 Chain F: Y.71, E.168, F.170, D.171, A.172 Ligand excluded by PLIP SIN.64: 6 residues within 4Å: Chain F: D.5, S.8, V.9, Q.12, A.158 Ligands: MLI.71 Ligand excluded by PLIP SIN.65: 6 residues within 4Å: Chain E: V.220 Chain F: R.62, E.178, F.179, G.180, K.184 Ligand excluded by PLIP SIN.66: 12 residues within 4Å: Chain F: R.13, Y.14, S.15, L.154, V.157, A.158, L.162, D.163, A.164, V.165, P.166 Ligands: MLI.71 Ligand excluded by PLIP SIN.67: 3 residues within 4Å: Chain F: K.17, F.73, K.77 Ligand excluded by PLIP SIN.68: 7 residues within 4Å: Chain E: E.219 Chain F: A.30, K.34, V.53, S.55, H.83 Ligands: TLA.40 Ligand excluded by PLIP SIN.75: 3 residues within 4Å: Chain G: R.62, F.179 Chain H: T.218 Ligand excluded by PLIP SIN.76: 3 residues within 4Å: Chain G: Q.12, A.204, L.206 Ligand excluded by PLIP SIN.77: 4 residues within 4Å: Chain G: F.111, A.116, A.119, N.120 Ligand excluded by PLIP SIN.78: 7 residues within 4Å: Chain G: A.30, K.34, V.53, S.55, H.83 Chain H: E.219 Ligands: MLI.81 Ligand excluded by PLIP SIN.79: 6 residues within 4Å: Chain G: M.4, D.5, I.6 Chain H: K.32, A.159, M.160 Ligand excluded by PLIP SIN.85: 6 residues within 4Å: Chain H: K.17, F.73, N.74, E.75, R.76, K.77 Ligand excluded by PLIP SIN.86: 5 residues within 4Å: Chain G: E.219 Chain H: A.30, K.34, S.55, H.83 Ligand excluded by PLIP SIN.87: 5 residues within 4Å: Chain H: Q.12, A.204, G.205, L.206, P.207 Ligand excluded by PLIP SIN.88: 4 residues within 4Å: Chain H: T.26, A.27, E.28, E.29 Ligand excluded by PLIP SIN.89: 3 residues within 4Å: Chain H: R.62, F.179, K.184 Ligand excluded by PLIP

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

MLI.6: 7 residues within 4Å: Chain A: M.4, D.5, I.6 Chain B: K.32, A.159, M.160 Ligands: MLI.16 Ligand excluded by PLIP MLI.16: 4 residues within 4Å: Chain A: M.4 Chain B: A.159, M.160 Ligands: MLI.6 Ligand excluded by PLIP MLI.25: 7 residues within 4Å: Chain C: F.19, R.76, D.80, S.198, E.200 Chain E: F.73, R.76 Ligand excluded by PLIP MLI.26: 10 residues within 4Å: Chain C: F.73, N.74, K.77, V.165, P.166, I.167, E.168, G.169 Chain D: F.127 Chain E: E.200 Ligand excluded by PLIP MLI.27: 7 residues within 4Å: Chain C: R.13, Y.14, S.15, N.203, K.208, R.210 Chain D: R.110 Ligand excluded by PLIP MLI.28: 6 residues within 4Å: Chain C: L.11, Q.12, R.13, A.204, L.206, K.208 Ligand excluded by PLIP MLI.35: 6 residues within 4Å: Chain C: R.110 Chain D: R.13, Y.14, S.15, K.208, R.210 Ligand excluded by PLIP MLI.36: 2 residues within 4Å: Chain D: G.205 Ligands: SIN.33 Ligand excluded by PLIP MLI.37: 7 residues within 4Å: Chain C: K.32, M.160 Chain D: M.4, D.5, I.6, V.7, S.8 Ligand excluded by PLIP MLI.51: 10 residues within 4Å: Chain E: R.13, Y.14, S.15, N.203, K.208, R.210 Chain F: P.41, R.110 Ligands: CL.57, CL.74 Ligand excluded by PLIP MLI.52: 4 residues within 4Å: Chain E: M.4, D.5 Chain F: A.3, M.4 Ligand excluded by PLIP MLI.53: 8 residues within 4Å: Chain E: F.73, N.74, P.166, I.167, E.168, G.169 Chain F: S.43, F.127 Ligand excluded by PLIP MLI.54: 8 residues within 4Å: Chain E: V.9, Q.12, R.13, A.158, G.161, L.162, D.163 Ligands: SIN.44 Ligand excluded by PLIP MLI.69: 8 residues within 4Å: Chain F: A.89, K.90, T.91, H.139, M.142, T.187, L.189 Chain H: V.199 Ligand excluded by PLIP MLI.70: 5 residues within 4Å: Chain E: K.34 Chain F: L.213, E.214, L.217, E.219 Ligand excluded by PLIP MLI.71: 8 residues within 4Å: Chain F: Q.12, R.13, A.158, G.161, L.162, D.163 Ligands: SIN.64, SIN.66 Ligand excluded by PLIP MLI.80: 8 residues within 4Å: Chain G: R.13, Y.14, S.15, N.203, K.208, R.210 Chain H: P.41, R.110 Ligand excluded by PLIP MLI.81: 2 residues within 4Å: Chain G: S.55 Ligands: SIN.78 Ligand excluded by PLIP MLI.90: 7 residues within 4Å: Chain G: P.41, R.110 Chain H: R.13, Y.14, S.15, K.208, R.210 Ligand excluded by PLIP

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

CL.7: 3 residues within 4Å: Chain A: A.96, W.97, R.100 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: G.169 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain A: R.110 Chain B: K.208, S.209, R.210 Ligands: FLC.10 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain C: R.13, Y.14, L.154, A.164, V.165 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain D: A.30, H.83 Ligand excluded by PLIP CL.56: 3 residues within 4Å: Chain E: P.212, L.213 Chain F: Q.38 Ligand excluded by PLIP CL.57: 6 residues within 4Å: Chain E: K.208, S.209, R.210 Chain F: R.110 Ligands: MLI.51, CL.74 Ligand excluded by PLIP CL.58: 4 residues within 4Å: Chain E: R.100 Chain F: L.211, P.212, T.215 Ligand excluded by PLIP CL.59: 3 residues within 4Å: Chain E: A.96, W.97, R.100 Ligand excluded by PLIP CL.73: 4 residues within 4Å: Chain E: Y.39 Chain F: A.10, R.13, K.208 Ligand excluded by PLIP CL.74: 5 residues within 4Å: Chain F: N.45, E.105, R.110 Ligands: MLI.51, CL.57 Ligand excluded by PLIP CL.83: 3 residues within 4Å: Chain G: N.74, G.169 Chain H: F.127 Ligand excluded by PLIP

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

NA.9: 2 residues within 4Å: Chain A: E.183, K.184 No protein-ligand interaction detected (PLIP) NA.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.60: 3 residues within 4Å: Chain E: T.56, E.57, E.58 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.57, E:E.58 NA.91: 3 residues within 4Å: Chain G: Q.38 Chain H: P.212, L.213 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:Q.38, H:L.213 Water bridges: G:Q.38, H:E.214

2 x FLC: CITRATE ANION(Non-covalent)

FLC.10: 10 residues within 4Å: Chain A: P.41, R.110 Chain B: R.13, Y.14, S.15, K.17, N.203, K.208, R.210 Ligands: CL.17 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.15, B:S.15, A:R.110, A:R.110 Water bridges: B:S.15, B:S.15 Salt bridges: B:R.13, B:K.17, B:K.208, B:R.210, A:R.110, A:R.110 FLC.30: 5 residues within 4Å: Chain C: Q.38 Chain D: P.212, L.213, E.214 Ligands: SIN.24 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:P.212 Hydrogen bonds: D:L.213, D:E.214, C:Q.38, C:Q.38

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

TLA.11: 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 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.74, B:N.74, B:K.77, B:E.168, B:G.169 Salt bridges: B:K.17, B:K.77, B:K.77 TLA.18: 5 residues within 4Å: Chain C: A.30, K.34, S.55, H.83 Chain D: E.219 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.34, C:S.55, C:S.55, D:E.219 Salt bridges: C:K.34, C:H.83 Water bridges: D:V.220 TLA.31: 10 residues within 4Å: Chain C: F.127 Chain D: 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 D Hydrogen bonds: D:N.74, D:N.74, D:E.168, D:G.169 Salt bridges: D:K.17, D:K.77 TLA.40: 4 residues within 4Å: Chain E: E.219, V.220 Chain F: S.55 Ligands: SIN.68 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.55, E:E.219 Water bridges: F:K.34, F:S.55, E:E.219 TLA.41: 4 residues within 4Å: Chain E: R.62, E.178, F.179, K.184 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.62, E:E.178, E:K.184 Salt bridges: E:R.62, E:K.184, E:K.184 TLA.61: 10 residues within 4Å: Chain E: F.127 Chain F: 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 F Hydrogen bonds: F:N.74, F:N.74, F:K.77, F:P.166, F:E.168, F:G.169 Water bridges: F:K.17 Salt bridges: F:K.17, F:K.77 TLA.84: 10 residues within 4Å: Chain G: S.43, F.127 Chain H: K.17, F.73, N.74, K.77, P.166, I.167, E.168, G.169 10 PLIP interactions: 8 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:N.74, H:N.74, H:K.77, H:E.168, H:G.169 Water bridges: H:K.17, G:T.44, G:T.44 Salt bridges: H:K.17, H:K.77

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

ACT.55: 5 residues within 4Å: Chain E: L.11, Q.12, A.204, L.206, K.208 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:K.208 ACT.72: 7 residues within 4Å: Chain F: D.176, A.177, G.180, L.181, K.182, E.183 Chain H: F.202 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.182, F:E.183 ACT.82: 3 residues within 4Å: Chain G: P.212, L.213 Chain H: Q.38 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:L.213, H:Q.38 Water bridges: G:E.214

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
A

D
B

E
C

F
D

G
G

H
H

Oxygen-insensitive NAD(P)H nitroreductase

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