SMTL ID : 5nqq.1

Rabbit Muscle L-lactate dehydrogenase in complex with NADH and oxaloacetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 30 residues within 4Å: Chain A: V.26, G.27, V.28, G.29, A.30, V.31, G.32, V.51, D.52, V.53, M.54, K.57, Y.83, T.95, A.96, G.97, R.99, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, Y.247, T.248, I.252 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.252, A:I.252 Hydrogen bonds: A:V.28, A:G.29, A:A.30, A:V.31, A:V.53, A:G.97, A:R.99, A:R.99, A:V.136, A:N.138, A:N.138 Water bridges: A:G.32, A:S.161 NAI.3: 34 residues within 4Å: Chain B: V.26, G.27, V.28, G.29, A.30, V.31, G.32, V.51, D.52, V.53, M.54, K.57, Y.83, T.95, A.96, G.97, A.98, R.99, Q.100, L.109, N.113, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, Y.247, T.248, I.252 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.31, B:I.252, B:I.252 Hydrogen bonds: B:G.29, B:A.30, B:V.31, B:V.53, B:K.57, B:G.97, B:A.98, B:N.113, B:V.136, B:N.138, B:N.138 Water bridges: B:G.32, B:R.99, B:Q.100, B:S.161 Salt bridges: B:K.57, B:R.99, B:R.99 NAI.5: 35 residues within 4Å: Chain C: V.26, G.27, V.28, G.29, A.30, V.31, G.32, V.51, D.52, V.53, M.54, K.57, Y.83, T.95, A.96, G.97, A.98, R.99, Q.100, L.109, N.113, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, Y.247, T.248, I.252 Ligands: OAA.6 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:V.31, C:I.252, C:I.252 Hydrogen bonds: C:A.30, C:V.31, C:D.52, C:V.53, C:K.57, C:G.97, C:N.113, C:V.136, C:N.138, C:N.138, C:H.193 Water bridges: C:G.29, C:G.32, C:Y.83, C:R.99, C:R.99, C:Q.100, C:S.161 Salt bridges: C:K.57, C:R.99, C:R.99 NAI.8: 32 residues within 4Å: Chain D: V.26, G.27, V.28, G.29, A.30, V.31, G.32, V.51, D.52, V.53, M.54, K.57, Y.83, T.95, A.96, G.97, N.113, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, Y.247, T.248, S.249, I.252 Ligands: OAA.9 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.31, D:I.252, D:I.252 Hydrogen bonds: D:V.28, D:A.30, D:V.31, D:D.52, D:V.53, D:K.57, D:G.97, D:V.136, D:N.138, D:N.138 Water bridges: D:G.29, D:G.32, D:S.161 Salt bridges: D:K.57

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

SO4.2: 6 residues within 4Å: Chain A: R.171, H.186, W.188 Chain C: L.183, S.184, H.186 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Water bridges: C:S.184, C:S.184, C:A.207, A:R.171, A:W.188, A:V.270, A:V.270 Salt bridges: C:H.186, A:R.171, A:H.186 SO4.4: 6 residues within 4Å: Chain B: R.171, H.186, W.188 Chain D: L.183, S.184, H.186 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:L.183 Water bridges: D:S.184, D:S.184, D:H.186, D:A.207, B:R.171, B:H.186, B:W.188 Salt bridges: D:H.186, B:R.171, B:H.186 SO4.7: 6 residues within 4Å: Chain A: L.183, S.184, H.186 Chain C: R.171, H.186, W.188 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Water bridges: C:R.171, C:W.188, A:H.186, A:A.207 Salt bridges: C:R.171, C:H.186, A:H.186 SO4.10: 6 residues within 4Å: Chain B: L.183, S.184, H.186 Chain D: R.171, H.186, W.188 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Water bridges: B:S.184, B:A.207, D:R.171, D:W.188 Salt bridges: B:H.186, D:R.171, D:H.186

2 x OAA: OXALOACETATE ION(Non-covalent)

OAA.6: 10 residues within 4Å: Chain C: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, I.242, T.248 Ligands: NAI.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:A.238 Hydrogen bonds: C:R.106, C:R.106, C:N.138, C:H.193, C:T.248, C:T.248, C:T.248 Water bridges: C:S.237, C:S.237 Salt bridges: C:R.106, C:R.169, C:H.193 OAA.9: 8 residues within 4Å: Chain D: N.138, L.165, R.169, H.193, A.238, I.242, T.248 Ligands: NAI.8 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.238 Hydrogen bonds: D:N.138, D:T.248 Water bridges: D:H.193, D:H.193, D:S.237, D:A.238 Salt bridges: D:R.169, D:H.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alam, M.T. et al., The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization. Nat Commun (2017)

Release Date

2017-06-07

Peptides

L-lactate dehydrogenase A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lactate dehydrogenase A chain

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