SMTL ID : 8s88.1 (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

2 x SFX: (3S)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine(Non-covalent)

SFX.1: 10 residues within 4Å: Chain A: W.149, G.153, L.154, P.155, K.156, H.157, M.277, K.279, E.287 Chain D: V.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.156, A:K.156 pi-Stacking: A:W.149 SFX.6: 11 residues within 4Å: Chain B: W.149, G.153, L.154, P.155, K.156, H.157, M.277, E.287 Chain C: V.12, A.13 Ligands: GOL.17 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.149, B:W.149, B:K.156 Hydrogen bonds: B:K.156, B:H.157, B:H.157, C:V.12

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.2: 10 residues within 4Å: Chain A: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, I.243, T.249 Ligands: NAI.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.107, A:N.139, A:T.249, A:T.249, A:T.249 Water bridges: A:A.239, A:T.249 Salt bridges: A:R.107, A:R.170, A:H.194 OXM.7: 10 residues within 4Å: Chain B: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, I.243, T.249 Ligands: NAI.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.107, B:N.139, B:T.249 Water bridges: B:A.239, B:T.249 Salt bridges: B:R.107, B:R.170, B:H.194 OXM.14: 9 residues within 4Å: Chain C: Q.101, R.107, N.139, L.166, R.170, H.194, A.239, T.249 Ligands: NAI.15 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.107, C:N.139, C:T.249, C:T.249 Water bridges: C:T.249 Salt bridges: C:R.107, C:R.170, C:H.194 OXM.20: 9 residues within 4Å: Chain D: Q.101, R.107, N.139, R.170, H.194, A.239, I.243, T.249 Ligands: NAI.21 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.107, D:N.139, D:T.249, D:T.249 Water bridges: 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.3: 29 residues within 4Å: Chain A: G.28, V.29, G.30, Q.31, V.32, G.33, 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.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.32, A:I.253 Hydrogen bonds: A:Q.31, A:V.32, A:G.33, A:D.53, A:V.54, A:G.98, A:V.99, A:N.114, A:V.137, A:N.139, A:N.139 Water bridges: A:T.96, A:R.100, A:R.100, A:Q.101 Salt bridges: A:R.100, A:R.100 NAI.8: 31 residues within 4Å: Chain B: V.27, 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, 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.7, GOL.9, PEG.13 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.32, B:I.253 Hydrogen bonds: B:Q.31, B:Q.31, B:V.32, B:D.53, B:V.54, B:Y.84, B:G.98, B:V.99, B:N.114, B:V.137, B:N.139, B:N.139, B:S.162 Water bridges: B:G.30, B:Q.101 Salt bridges: B:R.100, B:R.100 NAI.15: 32 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, Y.84, 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.14 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:V.32 Hydrogen bonds: C:Q.31, C:V.32, C:G.33, C:D.53, C:V.54, C:G.98, C:V.99, C:N.114, C:V.137, C:N.139, C:N.139, C:S.162 Water bridges: C:G.30, C:Q.31, C:Q.31, C:R.100, C:Q.101, C:Q.101 Salt bridges: C:R.100, C:R.100 NAI.21: 31 residues within 4Å: Chain D: 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, L.110, 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.20 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:V.32, D:I.253, D:I.253 Hydrogen bonds: D:V.29, D:Q.31, D:V.32, D:G.33, D:V.54, D:Y.84, D:G.98, D:V.99, D:N.114, D:V.137, D:N.139, D:N.139 Water bridges: D:G.30, D:Q.101 Salt bridges: D:R.100, D:R.100

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

BTB.4: 6 residues within 4Å: Chain A: G.104, S.106, D.196, V.236, E.237, Y.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.240 Salt bridges: A:D.196, A:E.237 BTB.16: 7 residues within 4Å: Chain C: G.104, E.105, S.106, D.196, V.236, E.237, Y.240 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.196, C:Y.240 Water bridges: C:S.106 Salt bridges: C:D.196, C:E.237 pi-Cation interactions: C:Y.240

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

SO4.5: 4 residues within 4Å: Chain A: R.172, H.187 Chain C: S.184, H.187 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Water bridges: A:R.172, A:H.187, A:W.189, A:I.271 Salt bridges: A:R.172, A:H.187, C:H.187 SO4.11: 3 residues within 4Å: Chain B: R.172, H.187 Chain D: H.187 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain D Water bridges: B:R.172, B:W.189, D:S.184, D:S.184, D:S.185, D:A.208 Salt bridges: B:R.172, B:H.187, D:H.187 SO4.12: 4 residues within 4Å: Chain B: S.184, H.187 Chain D: R.172, H.187 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Water bridges: D:R.172, D:R.172 Salt bridges: D:R.172, D:H.187, B:H.187 Hydrogen bonds: B:S.184 SO4.19: 4 residues within 4Å: Chain A: S.184, H.187 Chain C: R.172, H.187 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Water bridges: A:A.208, C:R.172, C:R.172, C:I.271 Salt bridges: A:H.187, C:R.172, C:H.187

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain B: Q.31, R.100, Y.248 Ligands: NAI.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.31, B:R.100, B:R.100 Water bridges: B:Q.31, B:Y.248 GOL.10: 9 residues within 4Å: Chain B: G.283, I.284, E.285, N.286, V.288, K.318, A.321, D.322, W.325 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.285, B:N.286, B:N.286, B:K.318 GOL.17: 6 residues within 4Å: Chain B: K.156 Chain C: P.11, V.12, A.13, E.14 Ligands: SFX.6 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.14, B:K.156, B:K.156 GOL.18: 7 residues within 4Å: Chain C: K.23, E.48, K.77, V.79, S.85, V.86, A.88 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.23, C:E.48, C:K.77, C:A.88 GOL.22: 5 residues within 4Å: Chain A: E.16 Chain D: P.155, H.157, R.158, R.299 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.158, D:R.299, A:E.16 Water bridges: D:D.131 GOL.23: 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:L.154, D:K.156 GOL.24: 4 residues within 4Å: Chain D: G.104, D.196, E.237, Y.240 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.104, D:E.237 GOL.25: 3 residues within 4Å: Chain D: Q.31, R.100, Y.248 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.31, D:R.100, D:R.100

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

PEG.13: 4 residues within 4Å: Chain B: R.113, N.116, V.117 Ligands: NAI.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.117 PEG.26: 4 residues within 4Å: Chain D: K.244, L.245, K.246, G.247 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
G

D
H

L-lactate dehydrogenase B chain

Related Entries With Identical Sequence