5W8L: Lactate Dehydrogenase A

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 59 and NADH. Determined by X-ray diffraction at 1.95 Å resolution. Released 17 Jan 2018.

Method
X-ray diffraction
Resolution
1.95 Å
Organism
Homo sapiens
Chains
4
Atoms
11,805
Mol. weight
152.69 kDa
Ligands
NAI, 9YA
Released
17 Jan 2018

Explore 5W8L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W8L contains 70 α-helices and 58 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 13 β-strands

ElementResiduesLengthSheet
α-helix3-75
β-strand21-2551
α-helix29-4012
β-strand46-5051
α-helix54-6613
α-helix68-703
β-strand75-7841
α-helix82-854
β-strand90-9341
α-helix97-1004
α-helix107-12620
α-helix1301
β-strand131-13441
α-helix139-15012
α-helix154-1563
β-strand157-15931
α-helix163-17715
α-helix181-1833
β-strand184-18962
β-strand19011
α-helix193-1953
β-strand197-20592
β-strand208-20922
α-helix210-2134
α-helix227-24418
α-helix249-26315
β-strand268-27581
β-strand287-29591
β-strand298-30251
α-helix309-32618
Chain B: 17 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix3-75
β-strand21-2553
α-helix29-4012
β-strand46-5053
α-helix54-6613
α-helix68-703
β-strand75-7843
α-helix82-854
β-strand90-9343
α-helix97-1004
α-helix105-12622
α-helix1301
β-strand131-13443
α-helix139-15012
α-helix154-1563
β-strand157-15933
α-helix163-17715
α-helix181-1833
β-strand184-18524
β-strand188-18925
β-strand19013
β-strand197-19825
α-helix200-2023
β-strand204-20524
β-strand208-20924
α-helix210-2134
α-helix227-24418
α-helix249-26315
β-strand268-27583
β-strand287-29593
β-strand298-30253
α-helix309-32618
Chains C and D: 18 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix3-75
β-strand21-2556
α-helix29-4012
β-strand46-5056
α-helix54-6613
α-helix68-703
β-strand75-7846
α-helix82-854
β-strand90-9346
α-helix97-1004
α-helix105-12622
α-helix1301
β-strand131-13446
α-helix139-15012
α-helix154-1563
β-strand157-15936
α-helix163-17715
α-helix181-1833
β-strand184-18527
β-strand188-18928
β-strand19016
α-helix193-1953
β-strand197-19828
α-helix200-2023
β-strand204-20527
β-strand208-20927
α-helix210-2134
α-helix227-24418
α-helix249-26315
β-strand268-27586
β-strand287-29596
β-strand298-30256
α-helix309-32618

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
L-lactate dehydrogenase A chainA, B, C, Dprotein332Homo sapiensP00338 (AlphaFold model)
Sequence of entity 1 (A, B, C, D), FASTA
>5W8L_1 L-lactate dehydrogenase A chain (chains A, B, C, D)
MATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKG
EMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFI
IPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGV
HPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYE
VIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGI
SDLVKVTLTSEEEARLKKSADTLWGIQKELQF

Ligands and cofactors

IDNameFormulaCopies
NAI1,4-dihydronicotinamide adenine dinucleotideC21 H29 N7 O14 P24
9YA2-{3-([1,1'-biphenyl]-3-yl)-5-(cyclopropylmethyl)-4-[(4-sulfamoylphenyl)methyl]…C30 H26 N4 O4 S24

Water and common crystallization additives (EDO) are not listed.

Primary citation

Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (LDH). Rai, G., Brimacombe, K.R., Mott, B.T. et al. J Med Chem (2017) 60:9184-9204. DOI 10.1021/acs.jmedchem.7b00941 · PubMed

Other PDB entries of the same protein (UniProt P00338 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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