6CDN: Cysteine dioxygenase type 1

Crystal structure of cysteine-bound ferrous form of the crosslinked Cl-Tyr157 human cysteine dioxygenase. Determined by X-ray diffraction at 2.06 Å resolution. Released 4 Jul 2018.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,688
Mol. weight: 23.63 kDa
Ligands: FE2, CYS
Released: 4 Jul 2018

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

Secondary structure: helices and β-sheets

6CDN 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	71-77	7	1
β-strand	82	1	2
α-helix	83-84	2
β-strand	85-86	2	2
β-strand	92-99	8	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	151-158	8	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

>6CDN_1 Cysteine dioxygenase type 1 (chains A)
SEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTR
NLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKK
SERVLRENQCAYINDSVGLHRVENISHTEPAVSLHLXSPPFDTCHAFDQRTGHKNKVTMT
FHSKFGIRTPNATSGSLENN

Ligands and cofactors

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

Water and common crystallization additives (GOL, 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…
6BPV 1.95 Å, Crystal structure of cysteine-bound ferrous form of the matured F2-Tyr157 human cysteine…
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…
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 6CDN 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.