SMTL ID : 3hzn.7 (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

10 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 3 residues within 4Å: Chain A: R.62, F.179 Chain B: T.218 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.62, A:K.184 SIN.2: 3 residues within 4Å: Chain A: Q.12, A.204, L.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.12 SIN.3: 4 residues within 4Å: Chain A: F.111, A.116, A.119, N.120 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.111, A:N.120 Hydrogen bonds: A:N.120 SIN.4: 7 residues within 4Å: Chain A: A.30, K.34, V.53, S.55, H.83 Chain B: E.219 Ligands: MLI.7 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.30 Salt bridges: A:K.34, A:K.34, A:H.83 Hydrogen bonds: B:E.219 SIN.5: 6 residues within 4Å: Chain A: M.4, D.5, I.6 Chain B: K.32, A.159, M.160 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.159, A:I.6 Salt bridges: B:K.32 SIN.11: 6 residues within 4Å: Chain B: K.17, F.73, N.74, E.75, R.76, K.77 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.77 Water bridges: B:R.76, B:R.76 Salt bridges: B:K.77, B:K.77 SIN.12: 5 residues within 4Å: Chain A: E.219 Chain B: A.30, K.34, S.55, H.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.55, B:S.55 Salt bridges: B:K.34, B:H.83 SIN.13: 5 residues within 4Å: Chain B: Q.12, A.204, G.205, L.206, P.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.12 Water bridges: B:K.208 SIN.14: 4 residues within 4Å: Chain B: T.26, A.27, E.28, E.29 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.26, B:E.28 Hydrogen bonds: B:T.26, B:A.27, B:E.28 SIN.15: 3 residues within 4Å: Chain B: R.62, F.179, K.184 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.62, B:K.184, B:K.184

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

MLI.6: 8 residues within 4Å: Chain A: R.13, Y.14, S.15, N.203, K.208, R.210 Chain B: P.41, R.110 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.15, A:S.15, A:N.203 Water bridges: A:S.15, B:R.110, B:R.110 Salt bridges: A:R.13, A:K.208, A:K.208, A:R.210, B:R.110 MLI.7: 2 residues within 4Å: Chain A: S.55 Ligands: SIN.4 No protein-ligand interaction detected (PLIP) MLI.16: 7 residues within 4Å: Chain A: P.41, R.110 Chain B: R.13, Y.14, S.15, K.208, R.210 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.15 Water bridges: B:S.15, 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

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

ACT.8: 3 residues within 4Å: Chain A: P.212, L.213 Chain B: Q.38 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.213, B:Q.38 Water bridges: A:E.214

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

CL.9: 3 residues within 4Å: Chain A: N.74, G.169 Chain B: F.127 Ligand excluded by PLIP

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

TLA.10: 10 residues within 4Å: Chain A: S.43, F.127 Chain B: K.17, F.73, N.74, K.77, P.166, I.167, E.168, G.169 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.74, B:N.74, B:K.77, B:E.168, B:G.169 Water bridges: B:K.17, A:T.44, A:T.44 Salt bridges: B:K.17, B:K.77

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

NA.17: 3 residues within 4Å: Chain A: Q.38 Chain B: P.212, L.213 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.213, A:Q.38 Water bridges: B:E.214, A:Q.38

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
G

B
H

Oxygen-insensitive NAD(P)H nitroreductase

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