SMTL ID : 8s88.3 (2 other biounits)

Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.1: 9 residues within 4Å: Chain A: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, T.249 Ligands: NAI.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.107, A:N.139, A:T.249 Water bridges: A:T.249 Salt bridges: A:R.107, A:R.170, A:H.194 OXM.4: 9 residues within 4Å: Chain B: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, T.249 Ligands: NAI.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.101, B:R.107, B:N.139, B:T.249, B:T.249 Water bridges: B:A.239, B:T.249 Salt bridges: B:R.107, B:R.170, B:H.194 OXM.9: 9 residues within 4Å: Chain C: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, T.249 Ligands: NAI.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.107, C:N.139, C:T.249 Water bridges: C:T.249 Salt bridges: C:R.107, C:R.170, C:H.194 OXM.16: 9 residues within 4Å: Chain D: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, T.249 Ligands: NAI.17 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.107, D:N.139, D:T.249, D:T.249 Salt bridges: D:R.107, D:R.170, D:H.194

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

NAI.2: 32 residues within 4Å: Chain A: V.27, G.28, V.29, G.30, Q.31, V.32, V.52, D.53, V.54, L.55, Y.84, T.96, A.97, G.98, V.99, R.100, Q.101, L.110, N.114, V.117, F.120, I.121, V.137, S.138, N.139, V.141, S.162, L.166, H.194, T.249, I.253 Ligands: OXM.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.32, A:I.253 Hydrogen bonds: A:Q.31, A:V.32, A:D.53, A:V.54, A:Y.84, A:G.98, A:V.99, A:Q.101, A:N.114, A:V.137, A:N.139, A:N.139, A:S.162 Water bridges: A:G.30, A:G.30, A:Q.101 Salt bridges: A:R.100, A:R.100 NAI.5: 31 residues within 4Å: Chain B: V.27, G.28, V.29, G.30, Q.31, V.32, G.33, V.52, D.53, V.54, L.55, Y.84, T.96, A.97, G.98, V.99, R.100, Q.101, N.114, V.117, I.121, V.137, S.138, N.139, V.141, S.162, L.166, H.194, T.249, I.253 Ligands: OXM.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.32 Hydrogen bonds: B:Q.31, B:V.32, B:G.33, B:D.53, B:V.54, B:G.98, B:V.99, B:N.114, B:V.137, B:N.139, B:N.139, B:S.162 Water bridges: B:Q.31, B:T.96 Salt bridges: B:R.100, B:R.100 NAI.10: 31 residues within 4Å: Chain C: V.27, G.28, V.29, G.30, Q.31, V.32, G.33, V.52, D.53, V.54, L.55, T.96, A.97, G.98, V.99, R.100, Q.101, N.114, V.117, F.120, I.121, V.137, S.138, N.139, V.141, S.162, L.166, H.194, T.249, I.253 Ligands: OXM.9 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:V.32, C:I.253 Hydrogen bonds: C:Q.31, C:V.32, C:G.33, C:V.54, C:Y.84, C:G.98, C:V.99, C:N.114, C:V.137, C:N.139, C:N.139 Water bridges: C:G.30, C:G.30, C:R.100, C:Q.101 Salt bridges: C:R.100, C:R.100 NAI.17: 30 residues within 4Å: Chain D: G.28, V.29, G.30, Q.31, V.32, V.52, D.53, V.54, L.55, T.96, A.97, G.98, V.99, R.100, Q.101, L.110, N.114, V.117, F.120, I.121, V.137, S.138, N.139, V.141, S.162, L.166, H.194, T.249, I.253 Ligands: OXM.16 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.253 Hydrogen bonds: D:Q.31, D:V.32, D:V.54, D:G.98, D:V.99, D:Q.101, D:N.114, D:V.137, D:N.139, D:N.139, D:S.162 Water bridges: D:G.30, D:G.33 Salt bridges: D:R.100, D:R.100

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

PEG.3: 5 residues within 4Å: Chain A: G.104, S.106, D.196, E.237, Y.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.104, A:E.237 Water bridges: A:S.106 PEG.14: 5 residues within 4Å: Chain C: M.281, Y.282, N.306, Q.307, K.308 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.282, C:K.308 Water bridges: C:G.283 PEG.15: 4 residues within 4Å: Chain C: V.54, L.55, E.56, D.57 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.56 Water bridges: C:K.58

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.6: 5 residues within 4Å: Chain B: G.104, S.106, D.196, E.237, Y.240 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.237, B:Y.240 Salt bridges: B:D.196, B:E.237 BTB.18: 6 residues within 4Å: Chain D: G.104, S.106, D.196, V.236, E.237, Y.240 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.237 Water bridges: D:E.237 Salt bridges: D:D.196, D:E.237

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain B: H.157, R.158, R.299 Chain C: E.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.299, C:E.16 Water bridges: B:R.158 GOL.8: 7 residues within 4Å: Chain B: K.43, S.44, L.45, K.266 Chain C: K.43, S.44, K.266 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:K.266, C:K.43, C:S.44, C:K.266, C:K.266 GOL.11: 11 residues within 4Å: Chain A: S.203, G.204, N.206, G.209, S.211 Chain C: S.203, G.204, V.205, N.206, G.209, S.211 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.203, C:S.203 Water bridges: C:V.205 GOL.19: 10 residues within 4Å: Chain B: S.203, G.204, N.206, G.209, S.211 Chain D: S.203, G.204, N.206, G.209, S.211 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.204, B:N.206, B:G.209, D:S.203, D:N.206 GOL.20: 3 residues within 4Å: Chain A: T.18 Chain D: N.267, N.297 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.267, D:N.297, D:N.297, A:T.18 GOL.21: 4 residues within 4Å: Chain D: W.149, L.154, P.155, K.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.149, D:K.156

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

SO4.12: 5 residues within 4Å: Chain A: S.184, S.185, H.187 Chain C: R.172, H.187 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:A.208 Salt bridges: A:H.187, C:R.172, C:H.187 SO4.13: 4 residues within 4Å: Chain A: R.172, H.187 Chain C: S.184, H.187 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Water bridges: A:R.172, C:A.208 Salt bridges: A:R.172, A:H.187, C:H.187 SO4.22: 4 residues within 4Å: Chain B: S.184, H.187 Chain D: R.172, H.187 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Water bridges: D:H.187, D:W.189, B:A.208 Salt bridges: D:R.172, D:H.187, B:H.187 Hydrogen bonds: B:S.184 SO4.23: 3 residues within 4Å: Chain B: R.172, H.187 Chain D: H.187 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Water bridges: B:G.188, D:A.208 Salt bridges: B:R.172, B:H.187, D:H.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Gysel, M. et al., Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and fluoxetine. To Be Published

Release Date

2025-03-19

Peptides

L-lactate dehydrogenase B chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
K

C
J

D
L

L-lactate dehydrogenase B chain

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