1KBI: Cytochrome B2

Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: Comparison with the Intact Wild-type Enzyme. Determined by X-ray diffraction at 2.3 Å resolution. Released 3 Apr 2002.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 7,863
Mol. weight: 115.63 kDa
Ligands: HEM, FMN, PO4, PYR
Released: 3 Apr 2002

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

Secondary structure: helices and β-sheets

1KBI contains 58 α-helices and 44 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: 32 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
α-helix	15-18	4
β-strand	20-21	2	2
β-strand	24-25	2	2
β-strand	26-29	4	3
β-strand	32-35	4	3
α-helix	40-42	3
α-helix	47-51	5
β-strand	57	1	3
α-helix	59-62	4
α-helix	63-65	3
α-helix	70-74	5
α-helix	77-79	3
β-strand	80-83	4	3
β-strand	84	1	1
β-strand	93	1	3
α-helix	103-114	12
α-helix	116-118	3
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	4
β-strand	178	1	5
β-strand	181-183	3	6
β-strand	186-188	3	6
β-strand	192-194	3	7
α-helix	195-196	2
α-helix	200-202	3
α-helix	209-217	9
β-strand	225-227	3	7
α-helix	235-240	6
β-strand	249-253	5	7
α-helix	259-272	14
β-strand	277-280	4	7
α-helix	290-297	8
α-helix	318-321	4
β-strand	323	1	8
β-strand	326	1	8
α-helix	332-341	10
β-strand	346-351	6	7
α-helix	354-362	9
β-strand	367-370	4	7
α-helix	381-383	3
α-helix	384-396	13
β-strand	401	1	9
β-strand	404	1	9
β-strand	405-409	5	7
α-helix	415-424	10
β-strand	428-431	4	7
α-helix	433-465	33
β-strand	469	1	5
α-helix	470-472	3
α-helix	475-477	3
β-strand	478-479	2	4
β-strand	486-487	2	10
α-helix	489-492	4
α-helix	494-499	6
α-helix	508-510	3

Chain B: 26 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	103-114	12
α-helix	116-118	3
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	11
β-strand	178	1	12
β-strand	181-183	3	13
β-strand	186-188	3	13
β-strand	192-194	3	14
α-helix	195-196	2
α-helix	200-202	3
α-helix	209-217	9
β-strand	225-227	3	14
α-helix	235-241	7
β-strand	249-253	5	14
α-helix	259-272	14
β-strand	277-280	4	14
α-helix	290-297	8
α-helix	317-321	5
α-helix	332-340	9
β-strand	346-351	6	14
α-helix	354-362	9
β-strand	367-370	4	14
β-strand	381	1	4
α-helix	382-383	2
α-helix	384-396	13
α-helix	400-402	3
β-strand	405-409	5	14
α-helix	415-424	10
β-strand	428-431	4	14
α-helix	433-465	33
β-strand	469	1	12
α-helix	470-472	3
α-helix	475-477	3
β-strand	478-479	2	11
β-strand	488-489	2	10
α-helix	490-492	3
α-helix	494-499	6
α-helix	508-510	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytochrome B2	A, B	protein	511	Saccharomyces cerevisiae	P00175 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1KBI_1 CYTOCHROME B2 (chains A, B)
EPKLDMNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTA
IFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPGETKEDIARKEQLKSLLPPLD
NIINLYDFEYLASQTLTKQAWAYYSSGANDEVTHRENHNAYHRIFFKPKILVDVRKVDIS
TDMLGSHVDVPFYVSATALCKLGNPLEGEKDVARGCGQGVTKVPQMISTLASCSPEEIIE
AAPSDKQIQWYQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQREKDMKLKFSNT
KAGPKAMKKTNVEESQGASRALSKFIDPSLTWKDIEELKKKTKLPIVIKGVQRTEDVIKA
AEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVFVDGGVRRGTDVLK
ALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDEIEMSMRLLGVTSIAELKPDLLDL
STLKARTVGVPNDVLYNEVYEGPTLTEFEDA

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	2
PO4	Phosphate ion	O4 P	1
PYR	Pyruvic acid	C3 H4 O3	1

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

Primary citation

Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme. Cunane, L.M., Barton, J.D., Chen, Z.W. et al. Biochemistry (2002) 41:4264-4272. DOI 10.1021/bi0119870 · PubMed

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

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…
1LDC 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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