6BPV: Cysteine dioxygenase type 1

Crystal structure of cysteine-bound ferrous form of the matured F2-Tyr157 human cysteine dioxygenase. Determined by X-ray diffraction at 1.95 Å resolution. Released 4 Jul 2018.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,770
Mol. weight: 23.45 kDa
Ligands: CYS, FE2
Released: 4 Jul 2018

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

Secondary structure: helices and β-sheets

6BPV contains 8 α-helices and 14 β-strands across 1 chain. 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: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	12-22	11
α-helix	30-39	10
α-helix	44-47	4
α-helix	48-50	3
β-strand	59-64	6	1
α-helix	66-68	3
β-strand	72-77	6	1
β-strand	82	1	2
α-helix	83-84	2
β-strand	85-86	2	2
β-strand	93-99	7	1
β-strand	102-107	6	2
α-helix	108-110	3
β-strand	119-124	6	2
α-helix	125-126	2
β-strand	130-133	4	1
β-strand	139-144	6	2
β-strand	151-155	5	1
β-strand	163-167	5	2
β-strand	174-178	5	2
β-strand	183-184	2	1
β-strand	187-188	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cysteine dioxygenase type 1	A	protein	200	Homo sapiens	Q16878 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6BPV_1 Cysteine dioxygenase type 1 (chains A)
SEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTR
NLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKK
SERVLRENQCAYINDSVGLHRVENISHTEPAVSLHLXSPPFDTCHAFDQRTGHKNKVTMT
FHSKFGIRTPNATSGSLENN

Ligands and cofactors

ID	Name	Formula	Copies
CYS	Cysteine	C3 H7 N O2 S	1
FE2	FE (II) ion	Fe	1

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

Primary citation

Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase. Li, J., Griffith, W.P., Davis, I. et al. Nat Chem Biol (2018) 14:853-860. DOI 10.1038/s41589-018-0085-5 · PubMed

Other PDB entries of the same protein (UniProt Q16878 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BPU 1.8 Å, Crystal structure of ferrous form of the F2-Tyr157 human cysteine dioxygenase with both…
6CDH 1.82 Å, Crystal structure of ferrous form of the Cl-Tyr157 human cysteine dioxygenase with both…
6E87 1.95 Å, Crystal structure of ferrous form of the crosslinked human cysteine dioxygenase in the…
6BPR 1.96 Å, Crystal structure of cysteine, nitric oxide-bound ferrous form of the uncrosslinked…
6CDN 2.06 Å, Crystal structure of cysteine-bound ferrous form of the crosslinked Cl-Tyr157 human…
6BPS 2.1 Å, Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human…
6BPX 2.15 Å, Crystal structure of cysteine-bound ferrous form of the matured Cl2-Tyr157 human…
6N42 2.2 Å, Crystal structure of cysteine-bound ferrous form of the crosslinked human cysteine…
6BGM 2.21 Å, Crystal structure of ferrous form of the crosslinked human cysteine dioxygenase
6BGF 2.25 Å, Crystal structure of cysteine-bound ferrous form of the crosslinked human cysteine…
6N43 2.29 Å, Crystal structure of cysteine, nitric oxide-bound ferrous form of the crosslinked human…
6BPT 2.4 Å, Crystal structure of ferrous form of the uncrosslinked F2-Tyr157 human cysteine…

Browse structure collections

About this viewer

MolViewer shows 6BPV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.