SMTL ID : 3wsw.1

Crystal structure of minor L-lactate dehydrogenase from Enterococcus mundtii in the ligands-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 17 residues within 4Å: Chain A: G.14, F.15, V.16, D.37, V.38, T.80, A.81, G.82, I.101, I.105, A.121, S.122, N.123, T.146, L.150, T.232, I.236 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.150, A:I.236, A:I.236 Hydrogen bonds: A:T.13, A:F.15, A:V.16, A:V.38, A:Y.68, A:G.82, A:A.121, A:N.123, A:N.123, A:T.146 Water bridges: A:G.14, A:G.17, A:Y.68, A:N.84, A:N.84 NAD.4: 18 residues within 4Å: Chain B: T.13, G.14, F.15, V.16, D.37, V.38, T.80, A.81, G.82, V.83, N.84, I.101, A.121, S.122, N.123, L.150, T.232, I.236 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.13, B:T.13, B:F.15, B:V.16, B:V.38, B:G.82, B:G.82, B:V.83, B:N.84, B:A.121, B:N.123 Water bridges: B:G.14, B:T.80 NAD.7: 17 residues within 4Å: Chain C: T.13, G.14, F.15, V.16, D.37, V.38, T.80, A.81, G.82, N.84, I.101, I.105, A.121, N.123, L.150, T.232, I.236 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:F.15, C:V.16, C:V.38, C:G.82, C:N.84, C:A.121, C:N.123, C:N.123 Water bridges: C:G.14, C:G.17, C:Q.104, C:R.154 NAD.9: 20 residues within 4Å: Chain D: T.13, G.14, F.15, V.16, D.37, V.38, T.80, A.81, G.82, N.98, I.101, I.105, A.121, S.122, N.123, V.125, T.146, L.150, T.232, I.236 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.236 Hydrogen bonds: D:T.13, D:F.15, D:V.16, D:V.38, D:G.82, D:N.98, D:A.121, D:N.123, D:N.123, D:T.146 Water bridges: D:G.14, D:G.17

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Q.252 Chain C: N.60 Chain D: A.160, L.161, A.164, V.165, P.167 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.252, C:N.60 Water bridges: C:V.63 GOL.5: 7 residues within 4Å: Chain A: N.60 Chain B: A.160, L.161, A.164, V.165, P.167 Chain C: Q.252 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.60, C:Q.252 GOL.6: 6 residues within 4Å: Chain B: Q.252 Chain C: L.161, V.165, P.167 Chain D: N.60, S.62 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.252, D:N.60, D:N.60

2 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.3: 12 residues within 4Å: Chain A: W.56 Chain B: R.156, R.168, S.169, H.171, Y.173 Chain C: R.156, R.168, S.169, H.171, Y.173 Chain D: W.56 16 PLIP interactions: 7 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:Y.173 Water bridges: C:Y.173, C:Y.173, C:Y.173, B:R.156, B:R.156, B:R.156, B:R.156, B:Y.173, B:V.254 Salt bridges: C:R.156, C:H.171, C:H.171, B:R.156, B:H.171, B:H.171 FBP.8: 10 residues within 4Å: Chain A: R.156, R.168, S.169, H.171, Y.173 Chain C: W.56 Chain D: R.156, R.168, H.171, Y.173 18 PLIP interactions: 11 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:Y.173 Water bridges: D:R.156, D:R.156, D:R.156, D:R.168, D:H.171, D:H.171, D:V.254, A:Y.173, A:Y.173, A:Y.173, A:Y.173 Salt bridges: D:R.156, D:H.171, D:H.171, A:R.156, A:H.171, A:H.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matoba, Y. et al., An alternative allosteric regulation mechanism of an acidophilic l-lactate dehydrogenase from Enterococcus mundtii 15-1A. Febs Open Bio (2014)

Release Date

2014-09-10

Peptides

L-lactate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lactate dehydrogenase

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