4OKN: L-lactate dehydrogenase A chain

Crystal structure of human muscle L-lactate dehydrogenase, ternary complex with NADH and oxalate. Determined by X-ray diffraction at 2.1 Å resolution. Released 3 Dec 2014.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 21,753
Mol. weight: 306.17 kDa
Ligands: NAI, OXL, KAN
Released: 3 Dec 2014

Explore 4OKN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OKN contains 137 α-helices and 122 β-strands across 8 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, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	9-11	3	1
β-strand	22-26	5	2
α-helix	30-41	12
β-strand	47-51	5	2
α-helix	55-67	13
α-helix	69-71	3
β-strand	76-79	4	2
α-helix	83-86	4
β-strand	91-94	4	2
α-helix	106-109	4
α-helix	110-127	18
α-helix	131	1
β-strand	132-135	4	2
α-helix	140-151	12
α-helix	155-157	3
β-strand	158-160	3	2
α-helix	164-178	15
α-helix	182-184	3
β-strand	185-190	6	3
β-strand	191	1	2
β-strand	198-206	9	3
β-strand	209-210	2	3
α-helix	211-214	4
α-helix	228-245	18
α-helix	250-264	15
β-strand	269-276	8	2
β-strand	288-296	9	2
β-strand	299-304	6	2
α-helix	310-327	18

Chain B: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	9-11	3	4
β-strand	22-26	5	5
α-helix	30-41	12
β-strand	47-51	5	5
α-helix	55-66	12
α-helix	69-71	3
β-strand	76-79	4	5
α-helix	83-86	4
β-strand	91-94	4	5
α-helix	98-100	3
α-helix	106-127	22
β-strand	132-135	4	5
α-helix	140-151	12
α-helix	155-157	3
β-strand	158-160	3	5
α-helix	164-178	15
α-helix	182-184	3
β-strand	185-186	2	6
β-strand	189-190	2	7
β-strand	191	1	5
β-strand	198-199	2	7
α-helix	201-203	3
β-strand	205-206	2	6
β-strand	209-210	2	6
α-helix	211-214	4
α-helix	228-245	18
α-helix	250-264	15
β-strand	269-276	8	5
β-strand	288-296	9	5
β-strand	299-304	6	5
α-helix	310-327	18

Chain C: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	9-11	3	5
α-helix	17-19	3
β-strand	22-26	5	4
α-helix	30-41	12
β-strand	47-51	5	4
α-helix	55-67	13
α-helix	69-71	3
β-strand	76-79	4	4
α-helix	83-86	4
β-strand	91-94	4	4
α-helix	106-109	4
α-helix	110-127	18
α-helix	131	1
β-strand	132-135	4	4
α-helix	140-151	12
α-helix	155-157	3
β-strand	158-160	3	4
α-helix	164-178	15
α-helix	182-184	3
β-strand	185-186	2	8
β-strand	189-190	2	9
β-strand	191	1	4
β-strand	198-199	2	9
α-helix	201-203	3
β-strand	205-206	2	8
β-strand	209-210	2	8
α-helix	211-214	4
α-helix	228-245	18
α-helix	250-264	15
β-strand	269-276	8	4
β-strand	288-296	9	4
β-strand	299-304	6	4
α-helix	310-327	18

Chain D: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	9-11	3	2
β-strand	22-26	5	1
α-helix	30-41	12
β-strand	47-51	5	1
α-helix	55-66	12
α-helix	69-71	3
β-strand	76-79	4	1
α-helix	83-86	4
β-strand	91-94	4	1
α-helix	106-109	4
α-helix	110-127	18
α-helix	131	1
β-strand	132-135	4	1
α-helix	140-151	12
α-helix	155-157	3
β-strand	158-160	3	1
α-helix	164-178	15
α-helix	182-184	3
β-strand	185-186	2	10
β-strand	189-190	2	11
β-strand	191	1	1
β-strand	198-199	2	11
α-helix	201-203	3
β-strand	205-206	2	10
β-strand	209-210	2	10
α-helix	211-214	4
α-helix	228-245	18
α-helix	250-264	15
β-strand	269-276	8	1
β-strand	288-296	9	1
β-strand	299-304	6	1
α-helix	305-306	2
α-helix	310-327	18

Chain E: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	9-11	3	12
β-strand	22-26	5	13
α-helix	30-41	12
β-strand	47-51	5	13
α-helix	55-67	13
α-helix	69-71	3
β-strand	76-79	4	13
α-helix	83-86	4
β-strand	91-94	4	13
α-helix	100-101	2
α-helix	106-109	4
α-helix	110-127	18
α-helix	131	1
β-strand	132-135	4	13
α-helix	140-151	12
α-helix	155-157	3
β-strand	158-160	3	13
α-helix	164-178	15
α-helix	182-184	3
β-strand	185-186	2	14
β-strand	189-190	2	15
β-strand	191	1	13
β-strand	198-199	2	15
α-helix	201-203	3
β-strand	205-206	2	14
β-strand	209-210	2	14
α-helix	211-214	4
α-helix	228-245	18
α-helix	250-264	15
β-strand	269-276	8	13
β-strand	288-296	9	13
β-strand	299-304	6	13
α-helix	310-328	19

Chain F: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	9-11	3	16
β-strand	22-26	5	17
α-helix	30-41	12
β-strand	47-51	5	17
α-helix	55-67	13
α-helix	69-71	3
β-strand	76-79	4	17
α-helix	83-86	4
β-strand	91-94	4	17
α-helix	100-101	2
α-helix	106-109	4
α-helix	110-127	18
α-helix	131	1
β-strand	132-135	4	17
α-helix	140-151	12
α-helix	155-157	3
β-strand	158-160	3	17
α-helix	164-178	15
α-helix	182-184	3
β-strand	185-190	6	18
β-strand	191	1	17
β-strand	198-206	9	18
β-strand	209-210	2	18
α-helix	211-214	4
α-helix	228-245	18
α-helix	250-265	16
β-strand	269-276	8	17
β-strand	288-296	9	17
β-strand	299-304	6	17
α-helix	310-327	18

Chain G: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	9-11	3	17
β-strand	22-26	5	16
α-helix	30-41	12
β-strand	47-51	5	16
α-helix	55-67	13
α-helix	69-71	3
β-strand	76-79	4	16
α-helix	83-86	4
β-strand	91-94	4	16
α-helix	106-109	4
α-helix	110-127	18
α-helix	131	1
β-strand	132-135	4	16
α-helix	140-151	12
α-helix	155-157	3
β-strand	158-160	3	16
α-helix	164-178	15
α-helix	182-184	3
β-strand	185-186	2	19
β-strand	189-190	2	20
β-strand	191	1	16
β-strand	198-199	2	20
α-helix	201-203	3
β-strand	205-206	2	19
β-strand	209-210	2	19
α-helix	211-214	4
α-helix	228-245	18
α-helix	250-264	15
β-strand	269-276	8	16
β-strand	288-296	9	16
β-strand	299-304	6	16
α-helix	310-327	18

Chain H: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	9-11	3	13
β-strand	22-26	5	12
α-helix	30-41	12
β-strand	47-51	5	12
α-helix	55-66	12
α-helix	69-71	3
β-strand	76-79	4	12
α-helix	83-86	4
β-strand	91-94	4	12
α-helix	100-101	2
α-helix	106-109	4
α-helix	110-127	18
α-helix	131	1
β-strand	132-135	4	12
α-helix	140-151	12
α-helix	155-157	3
β-strand	158-160	3	12
α-helix	164-178	15
α-helix	182-184	3
β-strand	185-190	6	21
β-strand	191	1	12
β-strand	198-206	9	21
β-strand	209-210	2	21
α-helix	211-214	4
α-helix	228-245	18
α-helix	250-264	15
β-strand	269-276	8	12
β-strand	288-296	9	12
β-strand	299-304	6	12
α-helix	310-327	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L-lactate dehydrogenase A chain	A, B, C, D, E, F, G, H	protein	337	Homo sapiens	P00338 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>4OKN_1 L-lactate dehydrogenase A chain (chains A, B, C, D, E, F, G, H)
ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGE
MMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFII
PNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVH
PLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEV
IKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGIS
DLVKVTLTSEEEARLKKSADTLWGIQKELQFHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAI	1,4-dihydronicotinamide adenine dinucleotide	C21 H29 N7 O14 P2	7
OXL	Oxalate ion	C2 O4	8
KAN	Kanamycin a	C18 H36 N4 O11	1

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

Primary citation

Structures of lactate dehydrogenase A (LDHA) in apo, ternary and inhibitor-bound forms. Kolappan, S., Shen, D.L., Mosi, R. et al. Acta Crystallogr D Biol Crystallogr (2015) 71:185-195. DOI 10.1107/S1399004714024791 · PubMed

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…
6MV8 1.95 Å, LDHA structure in complex with inhibitor 14
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…

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