SMTL ID : 5tjy.1

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with 2,6 Pyridine Dicarboxylic Acid and NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

PDC.1: 13 residues within 4Å: Chain A: T.78, P.104, N.105, H.133, H.134, K.137, D.139, S.142, G.143, T.144, A.193, F.218 Ligands: NAI.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.193, A:F.218 Hydrogen bonds: A:K.137, A:G.143, A:T.144, A:T.144, A:T.144 Water bridges: A:N.105, A:R.215 Salt bridges: A:H.133, A:H.133, A:H.134, A:K.137, A:K.137 pi-Cation interactions: A:H.133 PDC.15: 13 residues within 4Å: Chain B: T.78, P.104, N.105, H.133, H.134, K.137, D.139, S.142, G.143, T.144, A.193, F.218 Ligands: NAI.16 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.193, B:F.218 Hydrogen bonds: B:K.137, B:G.143, B:T.144, B:T.144, B:T.144 Water bridges: B:N.105, B:R.215 Salt bridges: B:H.133, B:H.133, B:H.134, B:K.137, B:K.137 pi-Cation interactions: B:H.133 PDC.29: 13 residues within 4Å: Chain C: T.78, P.104, N.105, H.133, H.134, K.137, D.139, S.142, G.143, T.144, A.193, F.218 Ligands: NAI.30 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.193, C:F.218 Hydrogen bonds: C:T.78, C:K.137, C:G.143, C:T.144, C:T.144 Water bridges: C:T.144, C:R.215 Salt bridges: C:H.133, C:H.133, C:H.134, C:K.137, C:K.137 pi-Cation interactions: C:H.133 PDC.43: 13 residues within 4Å: Chain D: T.78, P.104, N.105, H.133, H.134, K.137, D.139, S.142, G.143, T.144, A.193, F.218 Ligands: NAI.44 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.193, D:F.218 Hydrogen bonds: D:T.78, D:K.137, D:G.143, D:T.144, D:T.144 Water bridges: D:T.144, D:R.215 Salt bridges: D:H.133, D:H.133, D:H.134, D:K.137, D:K.137 pi-Cation interactions: D:H.133

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 23 residues within 4Å: Chain A: G.8, K.10, G.11, K.12, V.13, L.33, D.34, A.35, F.53, T.54, P.56, V.58, G.76, T.77, T.78, A.103, P.104, N.105, F.106, K.137, D.139, F.218 Ligands: PDC.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.13 Hydrogen bonds: A:G.8, A:K.10, A:K.12, A:V.13, A:A.35, A:G.76, A:T.78, A:F.106, A:D.139 Water bridges: A:G.14, A:G.36, A:N.62, A:T.78, A:D.139, A:R.215 Salt bridges: A:K.12, A:K.12 pi-Stacking: A:F.53, A:F.218 NAI.16: 23 residues within 4Å: Chain B: G.8, K.10, G.11, K.12, V.13, L.33, D.34, A.35, F.53, T.54, P.56, V.58, G.76, T.77, T.78, A.103, P.104, N.105, F.106, K.137, D.139, F.218 Ligands: PDC.15 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.13 Hydrogen bonds: B:G.8, B:K.10, B:K.12, B:V.13, B:A.35, B:G.76, B:T.78, B:F.106, B:D.139 Water bridges: B:G.14, B:G.36, B:N.62, B:T.78, B:D.139, B:R.215 Salt bridges: B:K.12, B:K.12 pi-Stacking: B:F.53, B:F.218 NAI.30: 23 residues within 4Å: Chain C: G.8, K.10, G.11, K.12, V.13, L.33, D.34, A.35, F.53, T.54, P.56, V.58, G.76, T.77, T.78, A.103, P.104, N.105, F.106, K.137, D.139, F.218 Ligands: PDC.29 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:V.13 Hydrogen bonds: C:G.8, C:K.10, C:K.12, C:V.13, C:A.35, C:G.76, C:T.78, C:F.106, C:D.139 Water bridges: C:G.14, C:G.36, C:N.62, C:D.139, C:R.215 Salt bridges: C:K.12, C:K.12 pi-Stacking: C:F.53, C:F.218 NAI.44: 23 residues within 4Å: Chain D: G.8, K.10, G.11, K.12, V.13, L.33, D.34, A.35, F.53, T.54, P.56, V.58, G.76, T.77, T.78, A.103, P.104, N.105, F.106, K.137, D.139, F.218 Ligands: PDC.43 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:V.13 Hydrogen bonds: D:G.8, D:K.10, D:K.12, D:V.13, D:A.35, D:G.76, D:T.78, D:F.106, D:D.139 Water bridges: D:G.14, D:G.36, D:N.62, D:D.139, D:R.215 Salt bridges: D:K.12, D:K.12 pi-Stacking: D:F.53, D:F.218

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

SO4.3: 5 residues within 4Å: Chain A: G.79, D.139, A.140, P.141 Chain D: T.168 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:L.170, A:P.141 SO4.17: 5 residues within 4Å: Chain B: G.79, D.139, A.140, P.141 Chain C: T.168 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:P.141, C:L.170 SO4.31: 5 residues within 4Å: Chain B: T.168 Chain C: G.79, D.139, A.140, P.141 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:L.170, C:P.141 SO4.45: 5 residues within 4Å: Chain A: T.168 Chain D: G.79, D.139, A.140, P.141 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:P.141, A:L.170

4 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.4: 4 residues within 4Å: Chain A: M.60, E.83, R.84 Ligands: IMD.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.83, A:R.84 BEZ.18: 4 residues within 4Å: Chain B: M.60, E.83, R.84 Ligands: IMD.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.83, B:R.84 BEZ.32: 4 residues within 4Å: Chain C: M.60, E.83, R.84 Ligands: IMD.33 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.83, C:R.84 BEZ.46: 4 residues within 4Å: Chain D: M.60, E.83, R.84 Ligands: IMD.47 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.83, D:R.84

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 5 residues within 4Å: Chain A: M.60, G.61, E.64, W.91 Ligands: BEZ.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.60 IMD.19: 5 residues within 4Å: Chain B: M.60, G.61, E.64, W.91 Ligands: BEZ.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:M.60 IMD.33: 5 residues within 4Å: Chain C: M.60, G.61, E.64, W.91 Ligands: BEZ.32 1 PLIP interactions: 1 interactions with chain C Water bridges: C:M.60 IMD.47: 5 residues within 4Å: Chain D: M.60, G.61, E.64, W.91 Ligands: BEZ.46 1 PLIP interactions: 1 interactions with chain D Water bridges: D:M.60

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

PG4.6: 10 residues within 4Å: Chain A: R.209, D.211 Chain B: H.194, E.196, R.209, D.211 Chain C: E.196, T.205, T.207 Ligands: PG4.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.209, B:R.209 PG4.20: 10 residues within 4Å: Chain A: H.194, E.196, R.209, D.211 Chain B: R.209, D.211 Chain D: E.196, T.205, T.207 Ligands: PG4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.209, A:R.209 PG4.34: 10 residues within 4Å: Chain A: E.196, T.205, T.207 Chain C: R.209, D.211 Chain D: H.194, E.196, R.209, D.211 Ligands: PG4.48 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.209, D:R.209 PG4.48: 10 residues within 4Å: Chain B: E.196, T.205, T.207 Chain C: H.194, E.196, R.209, D.211 Chain D: R.209, D.211 Ligands: PG4.34 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.209, C:R.209

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

NA.7: 4 residues within 4Å: Chain A: V.21, A.22, A.24, L.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.27 Water bridges: A:L.29 NA.21: 4 residues within 4Å: Chain B: V.21, A.22, A.24, L.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.22 Water bridges: B:L.29 NA.35: 4 residues within 4Å: Chain C: V.21, A.22, A.24, L.27 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.27 Water bridges: C:L.29 NA.49: 4 residues within 4Å: Chain D: V.21, A.22, A.24, L.27 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.24 Water bridges: D:L.29

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: R.122, F.123, F.124, D.125, T.201 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: N.46, T.47, G.70 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: R.174, G.175, A.176, D.177, P.182 Ligand excluded by PLIP EDO.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: D.177, D.179, G.180 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: N.162, P.163, D.164 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: R.122, F.123, F.124, D.125, T.201 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: N.46, T.47, G.70 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: R.174, G.175, A.176, D.177, P.182 Ligand excluded by PLIP EDO.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: D.177, D.179, G.180 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: N.162, P.163, D.164 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: R.122, F.123, F.124, D.125, T.201 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: N.46, T.47, G.70 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain C: R.174, G.175, A.176, D.177, P.182 Ligand excluded by PLIP EDO.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain C: D.177, D.179, G.180 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain C: N.162, P.163, D.164 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain D: R.122, F.123, F.124, D.125, T.201 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain D: N.46, T.47, G.70 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain D: R.174, G.175, A.176, D.177, P.182 Ligand excluded by PLIP EDO.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain D: D.177, D.179, G.180 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain D: N.162, P.163, D.164 Ligand excluded by PLIP

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

CL.14: 6 residues within 4Å: Chain A: V.111, M.114, R.147, G.238, L.239, E.240 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain B: V.111, M.114, R.147, G.238, L.239, E.240 Ligand excluded by PLIP CL.42: 6 residues within 4Å: Chain C: V.111, M.114, R.147, G.238, L.239, E.240 Ligand excluded by PLIP CL.56: 6 residues within 4Å: Chain D: V.111, M.114, R.147, G.238, L.239, E.240 Ligand excluded by PLIP

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
A

C
A

D
A

4-hydroxy-tetrahydrodipicolinate reductase

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