SMTL ID : 5us6.2 (2 other biounits)

Structure of Dihydrodipicolinate Reductase from Vibrio vulnificus Bound to NADH and 2,6 Pyridine Dicarboxylic Acid with Intact Polyhistidine Tag

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-tetramer

Ligands

3 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 21 residues within 4Å: Chain A: G.33, G.36, R.37, M.38, S.58, E.59, R.60, F.100, T.101, S.105, G.123, T.124, T.125, A.147, P.148, N.149, Y.150, K.184, D.186, F.264 Ligands: PDC.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.100, A:F.264 Hydrogen bonds: A:G.33, A:R.37, A:M.38, A:R.60, A:T.101, A:S.105, A:G.123, A:T.125, A:Y.150, A:D.186 Water bridges: A:R.37 Salt bridges: A:R.37, A:R.37 NAD.5: 21 residues within 4Å: Chain B: G.33, A.35, G.36, R.37, M.38, S.58, E.59, R.60, F.100, T.101, S.105, G.123, T.125, A.147, P.148, N.149, Y.150, K.184, D.186, F.264 Ligands: PDC.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.264 Hydrogen bonds: B:G.33, B:R.37, B:M.38, B:T.101, B:S.105, B:G.123, B:T.125, B:Y.150, B:K.184, B:D.186 Salt bridges: B:R.37, B:R.37 pi-Stacking: B:F.100 NAD.8: 22 residues within 4Å: Chain C: G.33, A.35, G.36, R.37, M.38, S.58, E.59, R.60, F.100, T.101, S.105, G.123, T.124, T.125, A.147, P.148, N.149, Y.150, K.184, D.186, F.264 Ligands: PDC.9 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.264 Hydrogen bonds: C:G.33, C:R.37, C:M.38, C:T.101, C:S.105, C:G.123, C:T.125, C:Y.150, C:K.184, C:D.186 Water bridges: C:R.37, C:R.37, C:R.261 Salt bridges: C:R.37, C:R.37 pi-Stacking: C:F.100

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

PDC.2: 11 residues within 4Å: Chain A: T.125, P.148, H.180, H.181, K.184, D.186, S.189, G.190, T.191, F.264 Ligands: NAD.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.264 Hydrogen bonds: A:K.184, A:G.190, A:T.191, A:T.191, A:T.191 Water bridges: A:V.238, A:R.261 Salt bridges: A:H.180, A:H.180, A:H.181, A:K.184, A:K.184 pi-Cation interactions: A:H.180 PDC.6: 11 residues within 4Å: Chain B: T.125, P.148, H.180, H.181, K.184, D.186, S.189, G.190, T.191, F.264 Ligands: NAD.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.264 Hydrogen bonds: B:T.125, B:K.184, B:D.186, B:G.190, B:T.191 Salt bridges: B:H.180, B:H.180, B:H.181, B:K.184, B:K.184 pi-Cation interactions: B:H.180 PDC.9: 10 residues within 4Å: Chain C: T.125, P.148, H.181, K.184, D.186, S.189, G.190, T.191, F.264 Ligands: NAD.8 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.264 Hydrogen bonds: C:K.184, C:G.190, C:T.191, C:T.191, C:T.191 Water bridges: C:R.261 Salt bridges: C:H.180, C:H.181, C:K.184, C:K.184 pi-Cation interactions: C:H.180

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: R.37, N.41, R.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.41 Salt bridges: A:R.261 SO4.4: 2 residues within 4Å: Chain A: K.163 Chain B: K.163 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.163, B:K.163 SO4.7: 3 residues within 4Å: Chain B: R.37, N.41, R.261 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.37, B:N.41, B:R.261 Salt bridges: B:R.261 SO4.10: 2 residues within 4Å: Chain C: N.41, R.261 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.41 Water bridges: C:R.261 Salt bridges: C:R.261 SO4.11: 2 residues within 4Å: Chain D: T.128, E.129 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.129 SO4.12: 6 residues within 4Å: Chain D: K.184, D.186, S.189, G.190, T.191 Ligands: SO4.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.186, D:G.190, D:T.191 Salt bridges: D:K.184 SO4.13: 4 residues within 4Å: Chain D: H.181, K.184, R.261 Ligands: SO4.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.261 Water bridges: D:V.185 Salt bridges: D:H.181, D:K.184 SO4.14: 3 residues within 4Å: Chain D: Q.115, Y.116, G.117 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.115 SO4.15: 2 residues within 4Å: Chain D: K.163, K.166 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.163, D:K.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pote, S. et al., Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus. Biochim Biophys Acta Gen Subj (2021)

Release Date

2018-02-21

Peptides

4-hydroxy-tetrahydrodipicolinate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

4-hydroxy-tetrahydrodipicolinate reductase

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