1BU5: Protein

X-ray crystal structure of the desulfovibrio vulgaris (hildenborough) apoflavodoxin-riboflavin complex. Determined by X-ray diffraction at 1.83 Å resolution. Released 9 Feb 1999.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Desulfovibrio vulgaris
Chains: 2
Atoms: 2,469
Mol. weight: 32.35 kDa
Ligands: RBF
Released: 9 Feb 1999

Explore 1BU5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BU5 contains 16 α-helices and 16 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.

Chains A and B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	14-28	15
β-strand	32-37	6	1
α-helix	38-40	3
β-strand	52-57	6	1
β-strand	59-60	2	2
β-strand	66-67	2	2
α-helix	72-76	5
α-helix	78-80	3
β-strand	87-94	8	1
α-helix	103-114	12
β-strand	118-119	2	1
α-helix	122-123	2
β-strand	124-127	4	1
α-helix	130-133	4
α-helix	134-147	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (flavodoxin)	A, B	protein	147	Desulfovibrio vulgaris	P00323 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1BU5_1 PROTEIN (FLAVODOXIN) (chains A, B)
PKALIVYGSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWG
DDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSYEYFCGAVDAIEEKLKNLGAEIVQ
DGLRIDGDPRAARDDIVGWAHDVRGAI

Ligands and cofactors

ID	Name	Formula	Copies
RBF	Riboflavin	C17 H20 N4 O6	2

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

Primary citation

X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex. Walsh, M.A., McCarthy, A., O'Farrell, P.A. et al. Eur J Biochem (1998) 258:362-371. DOI 10.1046/j.1432-1327.1998.2580362.x · PubMed

Other PDB entries of the same protein (UniProt P00323 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YOB 1.14 Å, Crystal Structure of flavodoxin without engineered disulfide bond
1F4P 1.3 Å, Y98W flavodoxin mutant 1.5A (D. Vulgaris)
1J8Q 1.35 Å, Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris Wild-type at 1.35…
5YOE 1.35 Å, Crystal Structure of flavodoxin with engineered disulfide bond A43C-L74C
5YOG 1.42 Å, Crystal Structure of flavodoxin with engineered disulfide bond N14C-C93
1J9E 1.44 Å, Low Temperature (100K) Crystal Structure of Flavodoxin D. vulgaris S35C Mutant at 1.44…
5YOC 1.5 Å, Crystal Structure of flavodoxin with engineered disulfide bond C102-R125C
1AKR 1.58 Å, G61A oxidized flavodoxin mutant
1WSW 1.69 Å, Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, dimer, semiquinone…
1XYY 1.7 Å, Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, homodimer, oxidised…
1AKW 1.75 Å, G61L oxidized flavodoxin mutant
1XYV 1.79 Å, Low Temperature (100K) Crystal Structure Of Flavodoxin Mutant S64C, monomer, semiquinone…

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