SMTL ID : 7epm.1

human LDHC complexed with NAD+ and ethylamino acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

4 x J9X: 2-(ethylamino)-2-oxidanylidene-ethanoic acid(Non-covalent)

J9X.1: 11 residues within 4Å: Chain A: R.100, Q.101, Q.102, N.139, L.166, R.170, H.194, A.239, I.243, T.249 Ligands: NAD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.139, A:H.194, A:T.249 Salt bridges: A:R.170, A:H.194 J9X.6: 11 residues within 4Å: Chain B: R.100, Q.101, Q.102, N.139, L.166, R.170, H.194, A.239, I.243, T.249 Ligands: NAD.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.139, B:H.194, B:T.249 Salt bridges: B:R.170, B:H.194 J9X.14: 11 residues within 4Å: Chain C: R.100, Q.101, Q.102, N.139, L.166, R.170, H.194, A.239, I.243, T.249 Ligands: NAD.15 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.139, C:H.194, C:T.249 Salt bridges: C:R.170, C:H.194 J9X.19: 11 residues within 4Å: Chain D: R.100, Q.101, Q.102, N.139, L.166, R.170, H.194, A.239, I.243, T.249 Ligands: NAD.20 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.139, D:H.194, D:T.249 Salt bridges: D:R.170, D:H.194

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

NAD.2: 36 residues within 4Å: Chain A: V.27, G.28, T.29, G.30, A.31, V.32, G.33, V.52, D.53, V.54, A.55, K.58, Y.84, T.96, A.97, G.98, A.99, R.100, Q.101, N.114, I.117, S.120, I.121, V.137, S.138, N.139, V.141, S.162, G.163, L.166, R.170, H.194, Y.248, T.249, I.253 Ligands: J9X.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.253 Hydrogen bonds: A:A.31, A:V.32, A:D.53, A:V.54, A:A.55, A:K.58, A:G.98, A:Q.101, A:N.114, A:S.120, A:S.120, A:V.137, A:N.139, A:N.139, A:S.162 Water bridges: A:G.33 Salt bridges: A:K.58, A:R.100, A:R.100 NAD.7: 35 residues within 4Å: Chain B: V.27, G.28, T.29, G.30, A.31, V.32, G.33, V.52, D.53, V.54, A.55, K.58, Y.84, T.96, A.97, G.98, A.99, R.100, Q.101, N.114, I.117, S.120, I.121, V.137, S.138, N.139, V.141, S.162, G.163, L.166, H.194, Y.248, T.249, I.253 Ligands: J9X.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.253 Hydrogen bonds: B:A.31, B:V.32, B:G.33, B:D.53, B:V.54, B:K.58, B:G.98, B:A.99, B:Q.101, B:N.114, B:S.120, B:S.120, B:V.137, B:N.139, B:S.162 Salt bridges: B:K.58, B:R.100, B:R.100 NAD.15: 36 residues within 4Å: Chain C: V.27, G.28, T.29, G.30, A.31, V.32, G.33, V.52, D.53, V.54, A.55, K.58, Y.84, T.96, A.97, G.98, A.99, R.100, Q.101, N.114, I.117, S.120, I.121, V.137, S.138, N.139, V.141, S.162, G.163, L.166, R.170, H.194, Y.248, T.249, I.253 Ligands: J9X.14 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.253 Hydrogen bonds: C:A.31, C:V.32, C:D.53, C:V.54, C:A.55, C:K.58, C:G.98, C:Q.101, C:N.114, C:S.120, C:S.120, C:V.137, C:N.139, C:N.139, C:S.162 Water bridges: C:G.33 Salt bridges: C:K.58, C:R.100, C:R.100 NAD.20: 35 residues within 4Å: Chain D: V.27, G.28, T.29, G.30, A.31, V.32, G.33, V.52, D.53, V.54, A.55, K.58, Y.84, T.96, A.97, G.98, A.99, R.100, Q.101, N.114, I.117, S.120, I.121, V.137, S.138, N.139, V.141, S.162, G.163, L.166, H.194, Y.248, T.249, I.253 Ligands: J9X.19 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.253 Hydrogen bonds: D:A.31, D:V.32, D:G.33, D:D.53, D:V.54, D:K.58, D:G.98, D:A.99, D:Q.101, D:N.114, D:S.120, D:S.120, D:V.137, D:N.139, D:S.162 Salt bridges: D:K.58, D:R.100, D:R.100

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

SO4.3: 5 residues within 4Å: Chain A: V.54, A.55, E.56, D.57, K.58 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: W.149, L.154, P.155, V.156 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain A: R.172, H.187, W.189, R.270 Chain B: T.184, S.185, H.187 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: V.54, A.55, E.56, D.57 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: G.81, K.82, D.83 Ligand excluded by PLIP SO4.10: 7 residues within 4Å: Chain A: T.184, S.185, H.187 Chain B: R.172, H.187, W.189, R.270 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: S.203, K.213, N.310 Ligands: SO4.12 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: N.310, S.311 Ligands: SO4.11 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: W.149, L.154, P.155, V.156 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain C: V.54, A.55, E.56, D.57, K.58 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: W.149, L.154, P.155, V.156 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain C: R.172, H.187, W.189, R.270 Chain D: T.184, S.185, H.187 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain D: V.54, A.55, E.56, D.57 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain D: G.81, K.82, D.83 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain C: T.184, S.185, H.187 Chain D: R.172, H.187, W.189, R.270 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain D: S.203, K.213, N.310 Ligands: SO4.25 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain D: N.310, S.311 Ligands: SO4.24 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain D: W.149, L.154, P.155, V.156 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, H. et al., Identification of human LDHC4 as a potential target for anticancer drug discovery. Acta Pharm Sin B (2022)

Release Date

2022-03-02

Peptides

L-lactate dehydrogenase C chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

L-lactate dehydrogenase C chain