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Structure of the rieske non-heme iron oxygenase gxta with dideoxysaxitoxin bound

Analyse Structure of the rieske non-heme iron oxygenase gxta with dideoxysaxitoxin bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WND
Type: protein
Length: 955 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sxtdiox
UniProt: C3RVP5
Ligands: FES, U5A, FE, CL
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sxtdiox	protein	311	23% helix, 33% strand	C3RVP5
B	Sxtdiox	protein	320	22% helix, 34% strand	C3RVP5
C	Sxtdiox	protein	324	20% helix, 33% strand	C3RVP5

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
U5A · [(2Z,3aS,4R,6Z,10aR)-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate · ligand · 3 copies · chains A, B, C
FE · Fe (III) ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 4 copies · chains A, C
GOL · Glycerol · additive · 14 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	558	0.80	0.86	53	U5A
2	312	0.78	0.89	39	U5A
3	372	0.78	0.87	44	U5A
4	168	0.58	0.82	27	empty
5	319	0.57	0.76	37	GOL

Interfaces

3 interfaces between chains.

B–C · 873 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 268 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 260 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6WND · Structure of the Rieske non-heme iron oxygenase GxtA with dideoxysaxitoxin bound · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt C3RVP5
Elsewhere: RCSB PDB 6WND · PDBe 6WND · UniProt C3RVP5

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