6MV8: LDHA structure

LDHA structure in complex with inhibitor 14. Determined by X-ray diffraction at 1.95 Å resolution. Released 30 Oct 2019.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,187
Mol. weight: 152.06 kDa
Ligands: NAI, D3S, LAC
Released: 30 Oct 2019

Explore 6MV8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MV8 contains 63 α-helices and 63 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: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	1
α-helix	16-18	3
β-strand	21-25	5	2
α-helix	29-40	12
β-strand	46-50	5	2
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-78	4	2
α-helix	82-85	4
β-strand	90-93	4	2
α-helix	107-126	20
β-strand	131-134	4	2
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	2
α-helix	163-177	15
α-helix	181-183	3
β-strand	184-185	2	3
β-strand	188-190	3	2
β-strand	196-198	3	2
α-helix	200-202	3
β-strand	204-205	2	3
β-strand	208-209	2	3
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	2
β-strand	287-295	9	2
β-strand	298-303	6	2
α-helix	309-326	18

Chain B: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	4
β-strand	21-25	5	5
α-helix	29-40	12
β-strand	46-50	5	5
α-helix	54-65	12
α-helix	68-70	3
β-strand	75-79	5	5
α-helix	82-85	4
β-strand	90-93	4	5
α-helix	107-126	20
α-helix	130	1
β-strand	131-134	4	5
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	5
α-helix	163-177	15
α-helix	181-183	3
β-strand	185	1	6
β-strand	188-189	2	7
β-strand	190	1	5
β-strand	197-198	2	7
α-helix	200-202	3
β-strand	204-205	2	6
β-strand	208-209	2	6
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	5
β-strand	287-295	9	5
β-strand	298-303	6	5
α-helix	309-326	18

Chain C: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	5
β-strand	21-25	5	4
α-helix	29-40	12
β-strand	46-50	5	4
α-helix	54-66	13
α-helix	68-70	3
β-strand	76-78	3	4
α-helix	82-85	4
β-strand	90-93	4	4
α-helix	106-126	21
β-strand	131-134	4	4
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	4
α-helix	163-177	15
α-helix	181-183	3
β-strand	185	1	8
β-strand	188-189	2	9
β-strand	190	1	4
β-strand	197-198	2	9
α-helix	200-202	3
β-strand	204-205	2	8
β-strand	208-209	2	8
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	4
β-strand	287-295	9	4
β-strand	298-303	6	4
α-helix	309-327	19

Chain D: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	2
β-strand	21-25	5	1
α-helix	29-40	12
β-strand	46-50	5	1
α-helix	54-65	12
α-helix	68-70	3
β-strand	75-78	4	1
α-helix	82-85	4
β-strand	90-93	4	1
α-helix	105-126	22
α-helix	130	1
β-strand	131-134	4	1
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	1
α-helix	163-177	15
α-helix	181-183	3
β-strand	185	1	10
β-strand	188-189	2	11
β-strand	190	1	1
β-strand	197-198	2	11
α-helix	200-202	3
β-strand	204-205	2	10
β-strand	208-209	2	10
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	1
β-strand	287-295	9	1
β-strand	298-303	6	1
α-helix	309-326	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L-lactate dehydrogenase A chain	A, B, C, D	protein	332	Homo sapiens	P00338 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6MV8_1 L-lactate dehydrogenase A chain (chains A, B, C, D)
MATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKG
EMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFI
IPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGV
HPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYE
VIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGI
SDLVKVTLTSEEEARLKKSADTLWGIQKELQF

Ligands and cofactors

ID	Name	Formula	Copies
NAI	1,4-dihydronicotinamide adenine dinucleotide	C21 H29 N7 O14 P2	4
D3S	(6S)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(2-hydroxyphenyl)-6-phenyl-5,6-di…	C23 H17 Cl O4 S	3
LAC	Lactic acid	C3 H6 O3	1

Water and common crystallization additives (EPE, SO4) are not listed.

Primary citation

Structure-based Optimization of Potent, Cell-Active Hydroxylactam Inhibitors of Lactate Dehydrogenase. Wei, B., Robarge, K., Labadie, S.S. et al. To be published.

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

5W8J 1.55 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29
5W8K 1.6 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29 and…
5W8H 1.8 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 11
9BK2 1.85 Å, Crystal structure of Lactate dehydrogenase in complex with…
4JNK 1.9 Å, Lactate Dehydrogenase A in complex with inhibitor compound 22
4RLS 1.91 Å, Lactate Dehydrogenase in complex with inhibitor compound 47
5W8I 1.95 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 23 and…
5W8L 1.95 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 59 and…
6BB0 1.95 Å, Lactate Dehydrogenase in complex with inhibitor (R)-3-((2-chlorophenyl)thio)-6-(3-((4-flu…
6Q13 2.0 Å, Crystal structure of ldha in complex with compound NCGC00420737-09 at 2.00 a resolution
4QO8 2.0 Å, Lactate Dehydrogenase A in complex with substituted 3-Hydroxy-2-mercaptocyclohex-2-enone…
6MVA 2.02 Å, LDHA structure in complex with inhibitor 14

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