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X-ray crystal structure of E. COLI ydii complexed with undeca-2-one- CoA

Analyse X-ray crystal structure of E. COLI ydii complexed with undeca-2-one- CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K4B
Type: protein
Length: 1,088 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Esterase ydii
EC: 3.1.-.-
UniProt: P77781
Ligands: UOQ, CL
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Esterase ydii (EC 3.1.-.-)	protein	136	22% helix, 40% strand	P77781

Ligands and binding sites

UOQ · undeca-2-one coenzyme A · ligand · 13 copies · chains A, B, C, D, E, F, G, H
CL · Chloride ion · ion · 2 copies · chains A, E

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	971	0.79	0.81	90	CL, UOQ
2	901	0.79	0.81	90	CL, UOQ
3	439	0.73	0.83	47	UOQ
4	527	0.73	0.81	47	UOQ
5	445	0.73	0.82	47	UOQ

Interfaces

15 interfaces between chains.

C–D · 1190 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1167 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1165 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 1138 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 609 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4K4B · X-ray crystal structure of E. coli YdiI complexed with undeca-2-one-CoA · the same entry in another collection · chain H against H, TM-score 1.00
P77781 · AlphaFold monomer V2.0 prediction for 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (P77781) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P77781
Elsewhere: RCSB PDB 4K4B · PDBe 4K4B · UniProt P77781

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