SMTL ID : 5tej.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: G.9, A.11, G.12, R.13, M.14, S.34, E.35, R.36, F.76, T.77, S.81, G.99, T.100, T.101, A.123, P.124, N.125, Y.126, R.237 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.76 Hydrogen bonds: A:G.9, A:R.13, A:M.14, A:T.77, A:S.81, A:G.99, A:T.101, A:Y.126 Water bridges: A:G.15, A:S.81, A:R.237 Salt bridges: A:R.13, A:R.13 NAD.3: 22 residues within 4Å: Chain B: G.9, A.11, G.12, R.13, M.14, S.34, E.35, R.36, F.76, T.77, S.81, G.99, T.100, T.101, A.123, P.124, N.125, Y.126, K.160, D.162, F.240 Ligands: 7FN.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.240 Hydrogen bonds: B:G.9, B:R.13, B:M.14, B:R.36, B:T.77, B:S.81, B:G.99, B:T.101, B:Y.126, B:K.160, B:D.162 Water bridges: B:R.13, B:R.13, B:R.13, B:G.15 Salt bridges: B:R.13, B:R.13 pi-Stacking: B:F.76 NAD.7: 22 residues within 4Å: Chain C: G.9, A.11, G.12, R.13, M.14, S.34, E.35, R.36, F.76, T.77, S.81, G.99, T.100, T.101, A.123, P.124, N.125, Y.126, K.160, D.162, F.240 Ligands: 7FN.8 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:F.240 Hydrogen bonds: C:G.9, C:R.13, C:M.14, C:T.77, C:S.81, C:G.99, C:T.101, C:Y.126, C:K.160, C:D.162 Water bridges: C:R.13, C:R.13, C:R.13, C:R.13, C:G.15, C:S.34 Salt bridges: C:R.13, C:R.13 pi-Stacking: C:F.76 NAD.10: 22 residues within 4Å: Chain D: G.9, A.11, G.12, R.13, M.14, S.34, E.35, R.36, F.76, T.77, S.81, G.99, T.100, T.101, A.123, P.124, N.125, Y.126, K.160, D.162, F.240 Ligands: 7FN.11 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:F.240 Hydrogen bonds: D:G.9, D:R.13, D:M.14, D:T.77, D:S.81, D:G.99, D:T.101, D:Y.126, D:K.160, D:D.162 Water bridges: D:A.11, D:G.12, D:R.13, D:R.13, D:R.13, D:R.13, D:R.13, D:G.15, D:S.34, D:T.101, D:T.101 Salt bridges: D:R.13, D:R.13 pi-Stacking: D:F.76

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

PG4.2: 8 residues within 4Å: Chain A: G.193, I.194 Chain C: G.102, F.103, A.163, P.164, I.169, Y.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.194

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

7FN.4: 9 residues within 4Å: Chain B: T.101, P.124, H.156, H.157, K.160, S.165, G.166, T.167 Ligands: NAD.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.166, B:T.167, B:T.167, B:T.167 Water bridges: B:R.237, B:R.237, B:R.237 Salt bridges: B:H.156, B:H.157, B:K.160, B:K.160 pi-Cation interactions: B:H.156 7FN.8: 9 residues within 4Å: Chain C: T.101, P.124, H.156, H.157, K.160, S.165, G.166, T.167 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.101, C:D.162, C:G.166, C:T.167 Water bridges: C:R.237, C:R.237 Salt bridges: C:H.156, C:H.157, C:K.160, C:K.160 pi-Cation interactions: C:H.156 7FN.11: 9 residues within 4Å: Chain D: T.101, P.124, H.156, H.157, K.160, S.165, G.166, T.167 Ligands: NAD.10 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.166, D:T.167, D:T.167, D:T.167, D:R.237 Water bridges: D:H.157, D:V.214 Salt bridges: D:H.156, D:H.156, D:H.157, D:K.160, D:K.160 pi-Cation interactions: D:H.156

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

NA.5: 4 residues within 4Å: Chain B: A.22, H.23, N.25, A.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.25 NA.9: 5 residues within 4Å: Chain C: A.22, H.23, H.24, N.25, A.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.22, C:A.28 NA.12: 4 residues within 4Å: Chain D: A.22, H.23, N.25, A.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.23 NA.13: 2 residues within 4Å: Chain D: G.180, N.181 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.180 Water bridges: D:N.181

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 9 residues within 4Å: Chain B: G.102, T.104, A.163, P.164, I.169, Y.189 Chain D: E.192, G.193, I.194 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.193, D:I.194

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