SMTL ID : 5kkc.1

l-lactate dehydrogenase from rabbit muscle with the inhibitor 6DHNAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-tetramer

Ligands

4 x 6V0: [[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

6V0.1: 33 residues within 4Å: Chain A: V.25, G.26, V.27, G.28, A.29, V.30, G.31, V.50, D.51, V.52, M.53, K.56, Y.82, T.94, A.95, G.96, A.97, R.98, Q.99, N.112, I.115, F.118, I.119, V.135, S.136, N.137, S.160, L.164, R.168, H.192, Y.246, T.247, I.251 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:V.30, A:I.251 Hydrogen bonds: A:V.27, A:A.29, A:V.30, A:V.52, A:G.96, A:A.97, A:Q.99, A:N.112, A:N.137, A:N.137, A:H.192 Water bridges: A:V.27, A:G.28, A:G.31, A:Y.82, A:R.98, A:R.98, A:R.98, A:R.98, A:Q.99 Salt bridges: A:R.98, A:R.98 6V0.4: 33 residues within 4Å: Chain B: V.25, G.26, V.27, G.28, A.29, V.30, G.31, V.50, D.51, V.52, M.53, K.56, Y.82, T.94, A.95, G.96, A.97, R.98, N.112, I.115, F.118, I.119, V.135, S.136, N.137, V.139, S.160, G.161, L.164, H.192, Y.246, T.247, I.251 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.30, B:V.135, B:I.251 Hydrogen bonds: B:V.27, B:A.29, B:V.30, B:V.52, B:G.96, B:R.98, B:N.112, B:N.137, B:N.137, B:S.160 Water bridges: B:G.28, B:G.31, B:G.161, B:R.168, B:H.192 Salt bridges: B:R.98, B:R.98 6V0.6: 34 residues within 4Å: Chain C: V.25, G.26, V.27, G.28, A.29, V.30, G.31, V.50, D.51, V.52, M.53, K.56, Y.82, T.94, A.95, G.96, A.97, R.98, Q.99, L.108, N.112, I.115, F.118, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, Y.246, T.247, I.251 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:V.30, C:V.135, C:I.251, C:I.251, C:I.251 Hydrogen bonds: C:A.29, C:V.30, C:D.51, C:V.52, C:K.56, C:G.96, C:N.112, C:N.137, C:N.137 Water bridges: C:G.28, C:G.31, C:R.98, C:Q.99, C:S.160, C:R.168, C:H.192 Salt bridges: C:K.56, C:R.98, C:R.98 6V0.8: 28 residues within 4Å: Chain D: G.26, V.27, G.28, A.29, V.30, G.31, D.51, V.52, T.94, A.95, G.96, A.97, R.98, Q.99, L.108, N.112, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, Y.246, T.247, I.251 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:V.30, D:I.251, D:I.251 Hydrogen bonds: D:V.27, D:G.28, D:A.29, D:V.30, D:D.51, D:G.96, D:A.97, D:N.112, D:N.137, D:N.137 Water bridges: D:G.31, D:R.98, D:Q.99, D:S.160, D:R.168, D:H.192, D:H.192 Salt bridges: D:R.98, D:R.98

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

SO4.2: 7 residues within 4Å: Chain A: G.281, I.282, K.283, E.284, K.316, A.319, D.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.281, A:K.283 Salt bridges: A:E.284, A:D.320 SO4.3: 5 residues within 4Å: Chain A: R.170, H.185, W.187 Chain D: S.183, H.185 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Water bridges: D:S.183, D:S.183, D:H.185, D:A.206, A:W.187 Salt bridges: D:H.185, A:R.170, A:H.185 SO4.5: 6 residues within 4Å: Chain B: R.170, H.185, W.187 Chain C: L.182, S.183, H.185 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Water bridges: C:S.183, C:S.183, C:A.206 Salt bridges: C:H.185, B:R.170, B:H.185 SO4.7: 6 residues within 4Å: Chain B: L.182, S.183, H.185 Chain C: R.170, H.185, W.187 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:L.182 Water bridges: B:S.183, B:S.183, B:A.206, C:W.187 Salt bridges: B:H.185, C:R.170, C:H.185 SO4.9: 5 residues within 4Å: Chain A: S.183, H.185 Chain D: R.170, H.185, W.187 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Water bridges: A:H.185, A:H.185, A:A.206 Salt bridges: A:H.185, D:R.170, D:H.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beaupre, B.A. et al., Ligand binding phenomena that pertain to the metabolic function of renalase. Arch.Biochem.Biophys. (2016)

Release Date

2016-11-02

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