Research workbench

Crystal structure of xaxb from xenorhabdus nematophil

Analyse Crystal structure of xaxb from xenorhabdus nematophil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GY7
Type: protein
Length: 1,329 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xaxb
UniProt: D3VB23
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 85% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xaxb	protein	337	86% helix, 0% strand	D3VB23
B, D	Xaxb	protein	338	83% helix, 1% strand	D3VB23
C	Xaxb	protein	316	86% helix, 1% strand	D3VB23

Pockets

14 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	440	0.73	0.82	40	empty
2	770	0.70	0.77	71	empty
3	85	0.69	0.93	20	empty
4	815	0.67	0.74	84	empty
5	162	0.59	0.83	25	empty

Interfaces

5 interfaces between chains.

A–D · 1414 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 943 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 339 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 31 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 29 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6GY7 · Crystal structure of XaxB from Xenorhabdus nematophil · 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 D3VB23
Elsewhere: RCSB PDB 6GY7 · PDBe 6GY7 · UniProt D3VB23

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.