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Crystal structure of the terminal component of the pah- hydroxylating dioxygenase from sphingomonas sp chy-1

Analyse Crystal structure of the terminal component of the pah- hydroxylating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2CKF
Type: protein
Length: 1,816 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ring-hydroxylating dioxygenase alpha subunit; Ring-hydroxylating dioxygenase beta subunit
UniProt: Q65AT1, Q65AT0
Ligands: FES, FE
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ring-hydroxylating dioxygenase alpha subunit	protein	448	34% helix, 25% strand	Q65AT1
B, D, F	Ring-hydroxylating dioxygenase beta subunit	protein	170	24% helix, 40% strand	Q65AT0
C	Ring-hydroxylating dioxygenase alpha subunit	protein	425	32% helix, 26% strand	Q65AT1
E	Ring-hydroxylating dioxygenase alpha subunit	protein	433	35% helix, 25% strand	Q65AT1

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, C, E
FE · Fe (III) ion · metal · 3 copies · chains A, C, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	970	0.85	0.86	138	empty
2	959	0.82	0.83	127	empty
3	370	0.81	0.90	42	empty
4	394	0.78	0.87	66	empty
5	82	0.75	0.97	19	empty

Interfaces

12 interfaces between chains.

A–B · 1734 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 1706 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 1635 Å² buried · 33 hydrogen bonds · protein-protein
A–C · 1585 Å² buried · 31 hydrogen bonds · protein-protein
C–E · 1513 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

2CKF · Crystal Structure of the Terminal Component of the PAH-hydroxylating Dioxygenase from… · 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 Q65AT1
Every structure of UniProt Q65AT0
Elsewhere: RCSB PDB 2CKF · PDBe 2CKF · UniProt Q65AT1 · UniProt Q65AT0

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