SMTL ID : 3kb6.1

Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-tetramer

Ligands

5 x PPI: PROPANOIC ACID(Non-covalent)

PPI.1: 7 residues within 4Å: Chain A: S.7, P.9, F.49, R.71, Y.297, L.303, I.306 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.297, A:L.303 Water bridges: A:D.12, A:R.71 Salt bridges: A:R.71 PPI.6: 7 residues within 4Å: Chain A: V.50, Y.51, D.76, R.231, E.260, E.261, H.294 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.51 Water bridges: A:V.50, A:H.77 Salt bridges: A:R.231, A:H.294 PPI.19: 6 residues within 4Å: Chain B: S.7, P.9, F.49, R.71, Y.297, I.306 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.71 PPI.30: 5 residues within 4Å: Chain C: S.7, P.9, F.49, R.71, Y.297 3 PLIP interactions: 3 interactions with chain C Water bridges: C:S.7, C:D.12 Salt bridges: C:R.71 PPI.37: 5 residues within 4Å: Chain D: S.7, P.9, F.49, R.71, Y.297 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.297 Water bridges: D:D.12 Salt bridges: D:R.71

4 x LAC: LACTIC ACID(Non-covalent)

LAC.2: 9 residues within 4Å: Chain A: F.49, S.72, V.73, G.74, Y.96, R.231, H.294, Y.297 Ligands: NAD.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.49, A:Y.297 Hydrogen bonds: A:V.73, A:G.74, A:Y.96, A:Y.96, A:R.231, A:R.231 Salt bridges: A:R.231 LAC.20: 9 residues within 4Å: Chain B: F.49, S.72, V.73, G.74, Y.96, R.231, H.294, Y.297 Ligands: NAD.21 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.49, B:Y.297 Hydrogen bonds: B:V.73, B:G.74, B:Y.96, B:R.231, B:R.231 Salt bridges: B:R.231 LAC.31: 9 residues within 4Å: Chain C: F.49, S.72, V.73, G.74, Y.96, R.231, H.294, Y.297 Ligands: NAD.32 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.49, C:Y.297 Hydrogen bonds: C:V.73, C:G.74, C:Y.96, C:R.231, C:R.231 Salt bridges: C:R.231 LAC.38: 9 residues within 4Å: Chain D: F.49, V.50, S.72, V.73, G.74, Y.96, R.231, H.294 Ligands: NAD.39 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.49, D:V.50 Hydrogen bonds: D:V.73, D:G.74, D:Y.96, D:Y.96, D:R.231, D:R.231 Salt bridges: D:R.231

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

NAD.3: 27 residues within 4Å: Chain A: V.73, Y.96, V.101, G.148, T.149, G.150, R.151, I.152, Y.170, D.171, V.172, H.201, V.202, P.203, E.207, T.208, T.229, A.230, R.231, D.255, V.256, H.294, A.296, Y.297 Ligands: LAC.2, GOL.11, PEG.14 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.73, A:V.101, A:I.152, A:Y.297 Hydrogen bonds: A:T.149, A:R.151, A:R.151, A:I.152, A:V.172, A:D.255, A:A.296, A:Y.297 Water bridges: A:D.76, A:D.76, A:G.150, A:Y.204, A:E.207 NAD.21: 24 residues within 4Å: Chain B: V.73, Y.96, V.101, T.149, G.150, R.151, I.152, Y.170, D.171, V.172, H.201, V.202, P.203, E.207, T.208, T.229, A.230, R.231, D.255, V.256, H.294, A.296, Y.297 Ligands: LAC.20 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.101, B:I.152, B:Y.297 Hydrogen bonds: B:T.149, B:T.149, B:R.151, B:R.151, B:I.152, B:V.172, B:D.255, B:D.255, B:Y.297 Water bridges: B:D.76, B:G.150, B:Y.204, B:Y.204 NAD.32: 25 residues within 4Å: Chain C: V.73, Y.96, V.101, T.149, G.150, R.151, I.152, Y.170, D.171, V.172, V.173, H.201, V.202, P.203, E.207, T.208, T.229, A.230, R.231, D.255, V.256, H.294, A.296, Y.297 Ligands: LAC.31 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:V.101, C:I.152, C:Y.297 Hydrogen bonds: C:T.149, C:T.149, C:R.151, C:R.151, C:I.152, C:V.172, C:D.255, C:D.255, C:A.296, C:Y.297 Water bridges: C:G.150, C:Y.204, C:R.231 NAD.39: 24 residues within 4Å: Chain D: V.73, Y.96, V.101, G.148, T.149, G.150, R.151, I.152, Y.170, D.171, V.172, H.201, V.202, P.203, T.208, T.229, A.230, R.231, D.255, V.256, H.294, A.296, Y.297 Ligands: LAC.38 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:V.101, D:I.152, D:Y.297 Hydrogen bonds: D:T.149, D:T.149, D:R.151, D:R.151, D:I.152, D:V.172, D:D.255, D:Y.297 Water bridges: D:D.76, D:G.150, D:Y.204, D:Y.204

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: R.137, D.196, K.221, D.222, G.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.137, A:R.137, A:D.196 PEG.7: 5 residues within 4Å: Chain A: P.63, L.65, K.66, K.86, G.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.66, A:G.87 PEG.9: 7 residues within 4Å: Chain A: F.75, D.76, I.78, D.79, L.80, D.81 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.79, A:D.79, A:L.80, A:D.81 PEG.14: 7 residues within 4Å: Chain A: T.149, G.150, D.171, V.173, R.175, Y.185 Ligands: NAD.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.149, A:V.173, A:R.175, A:Y.185 PEG.15: 5 residues within 4Å: Chain A: H.209, H.210, N.213, R.216 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.213, A:R.216 PEG.16: 3 residues within 4Å: Chain A: A.162, G.164 Ligands: 1PE.28 No protein-ligand interaction detected (PLIP) PEG.17: 11 residues within 4Å: Chain A: V.123, K.124, L.126 Chain B: L.281, C.285 Chain C: L.281, A.284, C.285 Chain D: V.123, K.124, L.126 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:L.281, B:L.281 PEG.29: 3 residues within 4Å: Chain C: K.179, V.184, Y.185 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.179, C:C.183, C:Y.185 Water bridges: C:E.176, C:E.176 PEG.36: 3 residues within 4Å: Chain C: Y.170, E.207, R.216 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.207, C:R.216 PEG.42: 3 residues within 4Å: Chain D: P.63, L.65, K.86 1 PLIP interactions: 1 interactions with chain D Water bridges: D:L.65

8 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 6 residues within 4Å: Chain A: Y.170, D.171, V.172, K.174, T.186, S.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174 1PE.8: 8 residues within 4Å: Chain A: T.143, K.166, L.168, V.184, E.190, E.194, D.196, K.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.143, A:K.166, A:E.190, A:E.194, A:K.221 1PE.10: 3 residues within 4Å: Chain A: E.37, L.58, K.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.61 1PE.13: 6 residues within 4Å: Chain A: E.99 Chain B: N.140, L.161, A.162, G.164 Ligands: 1PE.28 No protein-ligand interaction detected (PLIP) 1PE.23: 6 residues within 4Å: Chain B: S.33, V.35, E.37, E.57, L.58, K.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.61 1PE.24: 7 residues within 4Å: Chain B: Y.170, D.171, V.172, K.174, K.179, Y.185, T.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174 1PE.28: 7 residues within 4Å: Chain A: A.162 Chain B: M.158, Y.159, L.161, A.162 Ligands: 1PE.13, PEG.16 No protein-ligand interaction detected (PLIP) 1PE.34: 6 residues within 4Å: Chain C: Y.170, D.171, V.172, K.174, T.186, S.187 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.174 Water bridges: C:D.171, C:V.172, C:K.174

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 5 residues within 4Å: Chain A: E.207, M.211, R.216 Ligands: NAD.3, PEG.15 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.216, A:R.216 Water bridges: A:Y.170, A:E.207, A:T.208 GOL.12: 8 residues within 4Å: Chain A: K.53, L.54, T.55, D.76, H.77, I.78, D.79 Ligands: PEG.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.53, A:I.78 Water bridges: A:K.53, A:E.56 GOL.18: 5 residues within 4Å: Chain A: Y.51, I.264, L.265 Chain B: S.129, Q.130 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.130, B:Q.130 GOL.22: 6 residues within 4Å: Chain B: K.53, T.55, D.76, H.77, I.78, D.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.53, B:D.76 Water bridges: B:L.80 GOL.25: 3 residues within 4Å: Chain B: P.14, F.15, E.18 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.14, B:E.18 GOL.26: 7 residues within 4Å: Chain A: E.120, K.124 Chain B: K.117, D.121, A.284, C.285 Chain D: K.125 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:E.120, B:K.117 Hydrogen bonds: B:K.117 GOL.27: 6 residues within 4Å: Chain B: E.207, H.209, H.210, M.211, N.213, R.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.207, B:N.213 GOL.33: 2 residues within 4Å: Chain C: E.99 Chain D: G.164 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.162, C:E.99 GOL.35: 5 residues within 4Å: Chain C: T.55, D.76, H.77, I.78, D.79 No protein-ligand interaction detected (PLIP) GOL.40: 2 residues within 4Å: Chain D: D.222, R.246 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.246, D:R.246 Water bridges: D:K.248 GOL.41: 7 residues within 4Å: Chain D: K.53, L.54, T.55, D.76, H.77, I.78, D.79 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antonyuk, S.V. et al., Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate). Acta Crystallogr.,Sect.F (2009)

Release Date

2009-11-10

Peptides

D-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-lactate dehydrogenase