SMTL ID : 5ten.1 (1 other biounit)

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,5 Furan Dicarboxylic and NADH with Intact Polyhistidine Tag

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 18 residues within 4Å: Chain A: G.8, A.10, G.11, R.12, M.13, S.33, E.34, R.35, F.75, T.76, S.80, G.98, T.99, T.100, P.123, N.124, Y.125, F.239 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.8, A:R.12, A:M.13, A:T.76, A:T.100, A:Y.125 NAD.6: 22 residues within 4Å: Chain B: G.8, A.10, G.11, R.12, M.13, S.33, E.34, R.35, F.75, T.76, S.80, G.98, T.99, T.100, A.122, P.123, N.124, Y.125, K.159, D.161, F.239 Ligands: 7FN.7 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.239 Hydrogen bonds: B:G.8, B:R.12, B:M.13, B:R.35, B:T.76, B:S.80, B:G.98, B:T.100, B:Y.125, B:K.159, B:D.161 Water bridges: B:R.12, B:R.12, B:R.12, B:G.14, B:R.236 Salt bridges: B:R.12, B:R.12 pi-Stacking: B:F.75 NAD.9: 21 residues within 4Å: Chain C: G.8, A.10, G.11, R.12, M.13, S.33, E.34, R.35, F.75, T.76, S.80, G.98, T.100, A.122, P.123, N.124, Y.125, K.159, D.161, F.239 Ligands: 7FN.10 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:F.239 Hydrogen bonds: C:G.8, C:R.12, C:M.13, C:S.33, C:R.35, C:T.76, C:S.80, C:G.98, C:T.100, C:Y.125, C:K.159, C:D.161 Water bridges: C:R.12, C:R.12, C:G.14, C:R.236 Salt bridges: C:R.12, C:R.12 pi-Stacking: C:F.75 NAD.15: 21 residues within 4Å: Chain D: G.8, A.10, G.11, R.12, M.13, S.33, E.34, R.35, F.75, T.76, S.80, G.98, T.99, T.100, A.122, P.123, N.124, Y.125, K.159, F.239 Ligands: 7FN.16 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:F.239 Hydrogen bonds: D:G.8, D:R.12, D:M.13, D:T.76, D:S.80, D:G.98, D:T.100, D:Y.125, D:K.159, D:D.161 Water bridges: D:R.12, D:R.12, D:T.100, D:R.236 Salt bridges: D:R.12, D:R.12 pi-Stacking: D:F.75

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

SO4.2: 4 residues within 4Å: Chain A: H.156, K.159, R.236 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.236 Salt bridges: A:H.156, A:K.159 SO4.3: 6 residues within 4Å: Chain A: K.159, D.161, S.164, G.165, T.166 Ligands: SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.165, A:T.166 Water bridges: A:N.124, A:T.166 Salt bridges: A:K.159 SO4.4: 3 residues within 4Å: Chain A: R.12, N.16, R.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.12, A:N.16 Water bridges: A:R.236 SO4.5: 3 residues within 4Å: Chain A: H.156, H.158, R.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.158 Salt bridges: A:H.156, A:R.236 SO4.8: 2 residues within 4Å: Chain B: N.16, R.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.16, B:N.16 Salt bridges: B:R.236 SO4.11: 2 residues within 4Å: Chain C: R.157, H.158 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.157, C:H.158 SO4.12: 3 residues within 4Å: Chain C: R.12, N.16, R.236 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.16 Salt bridges: C:R.236 SO4.13: 5 residues within 4Å: Chain B: I.223, G.224 Chain C: M.237, T.238, N.241 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.241 SO4.17: 3 residues within 4Å: Chain D: R.12, N.16, R.236 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.16 Salt bridges: D:R.236

4 x 7FN: 2,5 Furan Dicarboxylic Acid(Non-covalent)

7FN.7: 9 residues within 4Å: Chain B: T.100, P.123, H.155, H.156, K.159, S.164, G.165, T.166 Ligands: NAD.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.165, B:T.166, B:T.166, B:T.166 Water bridges: B:H.156, B:R.236, B:R.236 Salt bridges: B:H.155, B:H.155, B:H.156, B:K.159, B:K.159 pi-Cation interactions: B:H.155 7FN.10: 9 residues within 4Å: Chain C: T.100, P.123, H.155, H.156, K.159, S.164, G.165, T.166 Ligands: NAD.9 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.100, C:D.161, C:G.165, C:T.166, C:R.236 Salt bridges: C:H.155, C:H.155, C:H.156, C:K.159, C:K.159 pi-Cation interactions: C:H.155 7FN.14: 6 residues within 4Å: Chain C: H.22, A.27, K.28, V.29, K.53, F.54 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.54 Hydrogen bonds: C:V.29, C:F.54 Salt bridges: C:H.22, C:H.22 pi-Stacking: C:F.54 7FN.16: 10 residues within 4Å: Chain D: T.100, P.123, H.155, H.156, K.159, D.161, S.164, G.165, T.166 Ligands: NAD.15 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.165, D:T.166, D:T.166, D:T.166 Water bridges: D:R.236 Salt bridges: D:H.155, D:H.155, D:H.156, D:K.159, D:K.159 pi-Cation interactions: D:H.155

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

2017-10-18

Peptides

4-hydroxy-tetrahydrodipicolinate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

4-hydroxy-tetrahydrodipicolinate reductase

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