SMTL ID : 1c3v.1

DIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND PDC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 20 residues within 4Å: Chain A: G.7, K.9, G.10, K.11, V.12, D.33, A.34, F.52, T.53, V.57, G.75, T.76, T.77, A.102, P.103, N.104, F.105, K.136, F.217 Ligands: PDC.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.12 Hydrogen bonds: A:K.9, A:K.11, A:V.12, A:G.75, A:T.77, A:F.105, A:K.136, A:K.136 Salt bridges: A:K.11, A:K.11 pi-Stacking: A:F.52, A:F.217 NDP.3: 21 residues within 4Å: Chain B: G.7, K.9, G.10, K.11, V.12, D.33, A.34, F.52, T.53, P.55, V.57, G.75, T.76, T.77, A.102, P.103, N.104, F.105, K.136, F.217 Ligands: PDC.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.12 Hydrogen bonds: B:K.9, B:K.11, B:V.12, B:G.75, B:T.77, B:F.105, B:K.136, B:K.136 Water bridges: B:G.13, B:R.214 Salt bridges: B:K.11, B:K.11 pi-Stacking: B:F.52, B:F.217 NDP.6: 20 residues within 4Å: Chain C: G.7, K.9, G.10, K.11, V.12, D.33, A.34, F.52, T.53, V.57, G.75, T.76, T.77, A.102, P.103, N.104, F.105, K.136, F.217 Ligands: PDC.7 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.12 Hydrogen bonds: C:K.9, C:K.11, C:V.12, C:G.75, C:T.77, C:F.105, C:K.136, C:K.136 Salt bridges: C:K.11, C:K.11 pi-Stacking: C:F.52, C:F.217 NDP.8: 21 residues within 4Å: Chain D: G.7, K.9, G.10, K.11, V.12, D.33, A.34, F.52, T.53, P.55, V.57, G.75, T.76, T.77, A.102, P.103, N.104, F.105, K.136, F.217 Ligands: PDC.9 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.12 Hydrogen bonds: D:K.9, D:K.11, D:V.12, D:G.75, D:T.77, D:F.105, D:K.136, D:K.136 Water bridges: D:G.13, D:R.214 Salt bridges: D:K.11, D:K.11 pi-Stacking: D:F.52, D:F.217

4 x PDC: PYRIDINE-2,6-DICARBOXYLIC ACID(Non-covalent)

PDC.2: 13 residues within 4Å: Chain A: T.77, P.103, N.104, H.132, H.133, K.136, D.138, S.141, G.142, T.143, A.192, F.217 Ligands: NDP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.192, A:F.217 Hydrogen bonds: A:T.77, A:K.136, A:G.142, A:T.143, A:T.143 Salt bridges: A:H.133, A:K.136, A:K.136 pi-Stacking: A:H.132 PDC.4: 13 residues within 4Å: Chain B: T.77, P.103, N.104, H.132, H.133, K.136, D.138, S.141, G.142, T.143, A.192, F.217 Ligands: NDP.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.192, B:F.217 Hydrogen bonds: B:K.136, B:G.142, B:T.143, B:T.143, B:T.143 Water bridges: B:R.214 Salt bridges: B:H.133, B:K.136, B:K.136 pi-Stacking: B:H.132 PDC.7: 13 residues within 4Å: Chain C: T.77, P.103, N.104, H.132, H.133, K.136, D.138, S.141, G.142, T.143, A.192, F.217 Ligands: NDP.6 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.192, C:F.217 Hydrogen bonds: C:T.77, C:K.136, C:G.142, C:T.143, C:T.143 Salt bridges: C:H.133, C:K.136, C:K.136 pi-Stacking: C:H.132 PDC.9: 13 residues within 4Å: Chain D: T.77, P.103, N.104, H.132, H.133, K.136, D.138, S.141, G.142, T.143, A.192, F.217 Ligands: NDP.8 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.192, D:F.217 Hydrogen bonds: D:K.136, D:G.142, D:T.143, D:T.143, D:T.143 Water bridges: D:R.214 Salt bridges: D:H.133, D:K.136, D:K.136 pi-Stacking: D:H.132

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 9 residues within 4Å: Chain A: T.204, T.206 Chain B: L.190, R.208, D.210 Chain C: H.193, R.208, D.210 Chain D: T.204 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: C:R.208, C:R.208, D:T.204, B:R.208, B:R.208 PG4.10: 9 residues within 4Å: Chain A: H.193, R.208, D.210 Chain B: T.204 Chain C: T.204, T.206 Chain D: L.190, R.208, D.210 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: D:R.208, D:R.208, A:R.208, A:R.208, B:T.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cirilli, M. et al., The three-dimensional structures of the Mycobacterium tuberculosisdihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity. Biochemistry (2003)

Release Date

2003-08-26

Peptides

DIHYDRODIPICOLINATE REDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

DIHYDRODIPICOLINATE REDUCTASE

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