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Crystal structure of pbsx exported protein xepa

Analyse Crystal structure of pbsx exported protein xepa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6I56
Type: protein
Length: 1,387 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phage-like element pbsx protein xepa
UniProt: P39797
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Phage-like element pbsx protein xepa	protein	276	2% helix, 53% strand	P39797
A	Phage-like element pbsx protein xepa	protein	279	2% helix, 53% strand	P39797
C	Phage-like element pbsx protein xepa	protein	278	2% helix, 54% strand	P39797
B, E	Phage-like element pbsx protein xepa	protein	277	2% helix, 53% strand	P39797

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains D, E, A, C, B

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

Pockets

20 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	179	0.83	0.97	48	empty
2	549	0.73	0.81	39	GOL
3	704	0.72	0.79	69	empty
4	106	0.61	0.87	26	empty
5	253	0.60	0.80	29	empty

Interfaces

10 interfaces between chains.

A–B · 3699 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 3582 Å² buried · 56 hydrogen bonds · protein-protein
C–E · 3528 Å² buried · 50 hydrogen bonds · protein-protein
D–E · 3498 Å² buried · 52 hydrogen bonds · protein-protein
D–B · 3457 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

6I56 · Crystal structure of PBSX exported protein XepA · the same entry in another collection · chain E against E, TM-score 1.00
P39797 · AlphaFold monomer V2.0 prediction for phage-like element pbsx protein xepa (P39797) · a predicted model of the same protein · chain D against A, TM-score 0.42

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 P39797
Elsewhere: RCSB PDB 6I56 · PDBe 6I56 · UniProt P39797

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