SMTL ID : 5tjz.1

Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with NADPH and 2,6 Pyridine Dicarboxylic Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: NAP.4 14 PLIP interactions: 14 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.134, A:K.137, A:K.137 pi-Cation interactions: A:H.133 PDC.19: 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: NAP.22 14 PLIP interactions: 14 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.134, B:K.137, B:K.137 pi-Cation interactions: B:H.133 PDC.37: 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: NAP.40 14 PLIP interactions: 14 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.134, C:K.137, C:K.137 pi-Cation interactions: C:H.133 PDC.55: 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: NAP.58 14 PLIP interactions: 14 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.134, D:K.137, D:K.137 pi-Cation interactions: D:H.133

4 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 4 residues within 4Å: Chain A: M.60, E.83, R.84 Ligands: IMD.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.83, A:R.84 BEZ.20: 4 residues within 4Å: Chain B: M.60, E.83, R.84 Ligands: IMD.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.83, B:R.84 BEZ.38: 4 residues within 4Å: Chain C: M.60, E.83, R.84 Ligands: IMD.39 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.83, C:R.84 BEZ.56: 4 residues within 4Å: Chain D: M.60, E.83, R.84 Ligands: IMD.57 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.83, D:R.84

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 5 residues within 4Å: Chain A: M.60, G.61, E.64, W.91 Ligands: BEZ.2 No protein-ligand interaction detected (PLIP) IMD.21: 5 residues within 4Å: Chain B: M.60, G.61, E.64, W.91 Ligands: BEZ.20 No protein-ligand interaction detected (PLIP) IMD.39: 5 residues within 4Å: Chain C: M.60, G.61, E.64, W.91 Ligands: BEZ.38 No protein-ligand interaction detected (PLIP) IMD.57: 5 residues within 4Å: Chain D: M.60, G.61, E.64, W.91 Ligands: BEZ.56 No protein-ligand interaction detected (PLIP)

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.4: 24 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, EDO.7 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.13, A:F.53, A:F.218 Hydrogen bonds: A:G.8, A:K.10, A:K.12, A:V.13, A:G.76, A:T.78, A:F.106, A:D.139 Water bridges: A:G.11, A:G.11, A:G.14, A:D.34, A:G.36, A:N.62, A:T.78, A:T.78, A:R.215 Salt bridges: A:K.12, A:K.12 NAP.22: 24 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.19, EDO.25 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:V.13, B:F.53, B:F.218 Hydrogen bonds: B:G.8, B:K.10, B:K.12, B:V.13, B:G.76, B:T.78, B:F.106, B:D.139 Water bridges: B:G.11, B:G.11, B:G.14, B:D.34, B:G.36, B:N.62, B:T.78, B:T.78, B:R.215 Salt bridges: B:K.12, B:K.12 NAP.40: 24 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.37, EDO.43 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:V.13, C:F.53, C:F.218 Hydrogen bonds: C:G.8, C:K.10, C:K.12, C:V.13, C:G.76, C:T.78, C:F.106, C:D.139 Water bridges: C:G.11, C:G.11, C:G.14, C:D.34, C:G.36, C:N.62, C:R.215 Salt bridges: C:K.12, C:K.12 NAP.58: 24 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.55, EDO.61 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:V.13, D:F.53, D:F.218 Hydrogen bonds: D:G.8, D:K.10, D:K.12, D:V.13, D:G.76, D:T.78, D:F.106, D:D.139 Water bridges: D:G.11, D:G.11, D:G.14, D:D.34, D:G.36, D:N.62, D:R.215 Salt bridges: D:K.12, D:K.12

4 x AE3: 2-(2-ETHOXYETHOXY)ETHANOL(Non-covalent)

AE3.5: 12 residues within 4Å: Chain A: D.211 Chain B: L.132, L.191, E.196, R.209, D.211 Chain C: I.130, E.196, L.198, T.205 Ligands: AE3.23, AE3.59 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.132, C:I.130 Hydrogen bonds: B:R.209, B:R.209 AE3.23: 12 residues within 4Å: Chain A: L.132, L.191, E.196, R.209, D.211 Chain B: D.211 Chain D: I.130, E.196, L.198, T.205 Ligands: AE3.5, AE3.41 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.130, A:L.132 Hydrogen bonds: A:R.209, A:R.209 AE3.41: 12 residues within 4Å: Chain A: I.130, E.196, L.198, T.205 Chain C: D.211 Chain D: L.132, L.191, E.196, R.209, D.211 Ligands: AE3.23, AE3.59 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.132, A:I.130 Hydrogen bonds: D:R.209, D:R.209 AE3.59: 12 residues within 4Å: Chain B: I.130, E.196, L.198, T.205 Chain C: L.132, L.191, E.196, R.209, D.211 Chain D: D.211 Ligands: AE3.5, AE3.41 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.130, C:L.132 Hydrogen bonds: C:R.209, C:R.209

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

CL.6: 5 residues within 4Å: Chain A: M.114, R.147, G.238, L.239, E.240 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: K.95, P.96, N.97, T.98 Ligands: EDO.10 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: T.81, A.82, K.150 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain B: M.114, R.147, G.238, L.239, E.240 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain B: K.95, P.96, N.97, T.98 Ligands: EDO.28 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: T.81, A.82, K.150 Ligand excluded by PLIP CL.42: 5 residues within 4Å: Chain C: M.114, R.147, G.238, L.239, E.240 Ligand excluded by PLIP CL.52: 5 residues within 4Å: Chain C: K.95, P.96, N.97, T.98 Ligands: EDO.46 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain C: T.81, A.82, K.150 Ligand excluded by PLIP CL.60: 5 residues within 4Å: Chain D: M.114, R.147, G.238, L.239, E.240 Ligand excluded by PLIP CL.70: 5 residues within 4Å: Chain D: K.95, P.96, N.97, T.98 Ligands: EDO.64 Ligand excluded by PLIP CL.71: 3 residues within 4Å: Chain D: T.81, A.82, K.150 Ligand excluded by PLIP

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

EDO.7: 8 residues within 4Å: Chain A: T.54, H.55, P.56, H.136, K.137, A.138 Ligands: NAP.4, EDO.8 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: H.55, H.136 Chain D: A.165 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: E.64, F.65, D.68 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: G.70, H.72, N.97, T.98 Ligands: CL.16 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: G.79, D.139, A.140, P.141 Chain D: T.168, L.170 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: N.162, D.164, R.174, G.180, P.182 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain C: F.123 Ligands: SO4.15, EDO.50 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: F.123, D.125, T.201 Ligands: EDO.49 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: H.55, D.57, V.58 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain B: T.54, H.55, P.56, H.136, K.137, A.138 Ligands: NAP.22, EDO.26 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: H.55, H.136 Chain C: A.165 Ligands: EDO.25 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: E.64, F.65, D.68 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: G.70, H.72, N.97, T.98 Ligands: CL.34 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: G.79, D.139, A.140, P.141 Chain C: T.168, L.170 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: N.162, D.164, R.174, G.180, P.182 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain D: F.123 Ligands: SO4.33, EDO.68 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: F.123, D.125, T.201 Ligands: EDO.67 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain B: H.55, D.57, V.58 Ligand excluded by PLIP EDO.43: 8 residues within 4Å: Chain C: T.54, H.55, P.56, H.136, K.137, A.138 Ligands: NAP.40, EDO.44 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain B: A.165 Chain C: H.55, H.136 Ligands: EDO.43 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain C: E.64, F.65, D.68 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain C: G.70, H.72, N.97, T.98 Ligands: CL.52 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain B: T.168, L.170 Chain C: G.79, D.139, A.140, P.141 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain C: N.162, D.164, R.174, G.180, P.182 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain A: F.123 Ligands: EDO.14, SO4.51 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain C: F.123, D.125, T.201 Ligands: EDO.13 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain C: H.55, D.57, V.58 Ligand excluded by PLIP EDO.61: 8 residues within 4Å: Chain D: T.54, H.55, P.56, H.136, K.137, A.138 Ligands: NAP.58, EDO.62 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain A: A.165 Chain D: H.55, H.136 Ligands: EDO.61 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain D: E.64, F.65, D.68 Ligand excluded by PLIP EDO.64: 5 residues within 4Å: Chain D: G.70, H.72, N.97, T.98 Ligands: CL.70 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain A: T.168, L.170 Chain D: G.79, D.139, A.140, P.141 Ligand excluded by PLIP EDO.66: 5 residues within 4Å: Chain D: N.162, D.164, R.174, G.180, P.182 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain B: F.123 Ligands: EDO.32, SO4.69 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain D: F.123, D.125, T.201 Ligands: EDO.31 Ligand excluded by PLIP EDO.72: 3 residues within 4Å: Chain D: H.55, D.57, V.58 Ligand excluded by PLIP

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

SO4.15: 6 residues within 4Å: Chain A: I.108, P.220, G.221, L.224, L.243 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Water bridges: A:F.106, A:I.108, A:G.221 SO4.33: 6 residues within 4Å: Chain B: I.108, P.220, G.221, L.224, L.243 Ligands: EDO.31 3 PLIP interactions: 3 interactions with chain B Water bridges: B:F.106, B:I.108, B:G.221 SO4.51: 6 residues within 4Å: Chain C: I.108, P.220, G.221, L.224, L.243 Ligands: EDO.49 3 PLIP interactions: 3 interactions with chain C Water bridges: C:F.106, C:I.108, C:G.221 SO4.69: 6 residues within 4Å: Chain D: I.108, P.220, G.221, L.224, L.243 Ligands: EDO.67 3 PLIP interactions: 3 interactions with chain D Water bridges: D:F.106, D:I.108, D:G.221

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

2018-01-10

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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