1LDC: L-lactate dehydrogenase

X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant crystallized in the presence of lactate or phenyl-lactate. Determined by X-ray diffraction at 2.9 Å resolution. Released 10 Jul 1995.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 6,961
Mol. weight: 115 kDa
Ligands: PYR, HEM, FMN
Released: 10 Jul 1995

Explore 1LDC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1LDC contains 59 α-helices and 36 β-strands across 2 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: 36 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
β-strand	26-29	4	1
β-strand	32-35	4	1
α-helix	40-42	3
α-helix	48-52	5
β-strand	57	1	1
α-helix	59-62	4
α-helix	63-65	3
α-helix	70-74	5
α-helix	77-79	3
β-strand	80-81	2	1
α-helix	82-84	3
α-helix	90-92	3
β-strand	93	1	1
α-helix	94-96	3
α-helix	103-105	3
α-helix	107-112	6
α-helix	117-118	2
α-helix	119-121	3
α-helix	125-135	11
α-helix	138-145	8
α-helix	152-159	8
α-helix	160-163	4
β-strand	165-166	2	2
β-strand	178	1	3
β-strand	181-182	2	4
β-strand	187-188	2	4
β-strand	192-194	3	5
α-helix	209-216	8
β-strand	225-228	4	5
α-helix	235-240	6
β-strand	249-253	5	5
α-helix	259-271	13
β-strand	277-280	4	5
α-helix	286-288	3
α-helix	290-295	6
α-helix	332-341	10
β-strand	346-351	6	5
α-helix	354-362	9
β-strand	367-370	4	5
α-helix	381-383	3
α-helix	384-397	14
α-helix	401-403	3
β-strand	405-409	5	5
α-helix	415-423	9
β-strand	428-431	4	5
α-helix	433-465	33
β-strand	469	1	3
α-helix	470-472	3
α-helix	475-477	3
β-strand	478-479	2	2
β-strand	486-487	2	6
α-helix	489-491	3
α-helix	494-499	6
α-helix	500-503	4
α-helix	506-508	3

Chain B: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	105-112	8
α-helix	119-121	3
α-helix	125-133	9
α-helix	138-145	8
α-helix	152-159	8
α-helix	160-163	4
β-strand	165-166	2	7
β-strand	178	1	8
β-strand	181-183	3	9
β-strand	186-188	3	9
β-strand	192-194	3	10
α-helix	200-202	3
α-helix	208-215	8
β-strand	225-228	4	10
α-helix	235-241	7
β-strand	249-253	5	10
α-helix	254-256	3
α-helix	259-271	13
β-strand	277-280	4	10
α-helix	290-293	4
α-helix	332-340	9
β-strand	346-351	6	10
α-helix	354-362	9
β-strand	367-370	4	10
β-strand	381	1	2
α-helix	382-383	2
α-helix	384-397	14
α-helix	400-403	4
β-strand	405-409	5	10
α-helix	415-424	10
β-strand	429-431	3	10
α-helix	433-465	33
β-strand	469	1	8
α-helix	470-472	3
α-helix	475-477	3
β-strand	478-479	2	7
β-strand	488-489	2	6
α-helix	494-499	6
α-helix	505-507	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L-lactate dehydrogenase	A, B	protein	511	Saccharomyces cerevisiae	P00175 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1LDC_1 L-LACTATE DEHYDROGENASE (chains A, B)
EPKLDMNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTA
IFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPGETKEDIARKEQLKSLLPPLD
NIINLYDFEYLASQTLTKQAWAFYSSGANDEVTHRENHNAYHRIFFKPKILVDVRKVDIS
TDMLGSHVDVPFYVSATALCKLGNPLEGEKDVARGCGQGVTKVPQMISTLASCSPEEIIE
AAPSDKQIQWYQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQREKDMKLKFSNT
KAGPKAMKKTNVEESQGASRALSKFIDPSLTWKDIEELKKKTKLPIVIKGVQRTEDVIKA
AEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVFVDGGVRRGTDVLK
ALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAELKPDLLDL
STLKARTVGVPNDVLYNEVYEGPTLTEFEDA

Ligands and cofactors

ID	Name	Formula	Copies
PYR	Pyruvic acid	C3 H4 O3	2
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	2

Primary citation

X-ray structure of two complexes of the Y143F flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl lactate. Tegoni, M., Begotti, S., Cambillau, C. Biochemistry (1995) 34:9840-9850. DOI 10.1021/bi00031a004 · PubMed

Other PDB entries of the same protein (UniProt P00175 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KBI 2.3 Å, Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast…
1FCB 2.4 Å, Molecular structure of flavocytochrome B2 at 2.4 Å resolution
1KBJ 2.5 Å, Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast…
1LTD 2.6 Å, The 2.6 Å refined structure of the escherichia coli recombinant saccharomyces cerevisiae…
1SZF 2.7 Å, A198G:L230A mutant flavocytochrome b2 with pyruvate bound
1SZG 2.7 Å, A198G:L230A flavocytochrome b2 with sulfite bound
3KS0 2.7 Å, Crystal structure of the heme domain of flavocytochrome b2 in complex with Fab B2B4
1QCW 2.75 Å, Flavocytochrome B2, ARG289LYS mutant
2OZ0 2.8 Å, Mechanistic and Structural Studies of H373Q Flavocytochrome b2: Effects of Mutating the…
1LCO 2.9 Å, X-ray structure of two complexes of the Y143F flavocytochrome B2 mutant crystallized in…
1SZE 3.0 Å, L230A mutant flavocytochrome b2 with benzoylformate
9J9B 3.83 Å, Substrate-engaged TIM23 complex from yeast

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