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Crystal structure of LIGU(K66M) bound to substrate

Analyse Crystal structure of LIGU(K66M) bound to substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P3H
Type: protein
Length: 1,405 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: (4E)-oxalomesaconate delta-isomerase
EC: 5.3.3.-
UniProt: Q0KJL4
Ligands: NQM, CL
Pockets: 10 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, B	(4E)-oxalomesaconate delta-isomerase (EC 5.3.3.-)	protein	351	21% helix, 35% strand	Q0KJL4
C	(4E)-oxalomesaconate delta-isomerase (EC 5.3.3.-)	protein	352	20% helix, 34% strand	Q0KJL4

Ligands and binding sites

NQM · (1E)-4-oxobut-1-ene-1,2,4-tricarboxylic acid · ligand · 4 copies · chains A, D, C, B
CL · Chloride ion · ion · 6 copies · chains A, D, C, B

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.73	0.98	22	NQM
2	581	0.73	0.80	73	NQM
3	53	0.72	0.99	19	NQM
4	53	0.71	0.98	19	NQM
5	603	0.69	0.78	67	empty

Interfaces

2 interfaces between chains.

A–C · 1554 Å² buried · 29 hydrogen bonds · protein-protein
D–B · 1549 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

6P3H · Crystal structure of LigU(K66M) bound to substrate · the same entry in another collection · chain A against A, TM-score 1.00
Q0KJL4 · AlphaFold monomer V2.0 prediction for (4E)-oxalomesaconate delta- isomerase (Q0KJL4) · a predicted model of the same protein · 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 Q0KJL4
Elsewhere: RCSB PDB 6P3H · PDBe 6P3H · UniProt Q0KJL4

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