MolNFT v1 · #138894 · protein

The crystal structure of vabb-icl domain from vibrio anguillarum 775

5WXV · Isochorismate lyase: “The crystal structure of vabb-icl domain from vibrio anguillarum 775”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #138894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WXV
Type: protein
Length: 2,376 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isochorismate lyase
UniProt: Q5DK16
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Isochorismate lyase	protein	198	38% helix, 18% strand	Q5DK16

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1068	0.79	0.80	98	empty
2	1025	0.73	0.77	80	empty
3	946	0.73	0.77	77	empty
4	136	0.69	0.89	23	empty
5	132	0.68	0.89	21	empty

Interfaces

15 interfaces between chains.

I–J · 1496 Å² buried · 19 hydrogen bonds · protein-protein
B–K · 1493 Å² buried · 19 hydrogen bonds · protein-protein
E–L · 1480 Å² buried · 17 hydrogen bonds · protein-protein
A–F · 1466 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1464 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5WXV · The crystal structure of VabB-ICL domain from Vibrio anguillarum 775 · 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 Q5DK16
Elsewhere: RCSB PDB 5WXV · PDBe 5WXV · UniProt Q5DK16

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