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Crystal structure of minor pseudopilin ternary complex of xcpvwx from the type 2 secretion system of pseudomonas aeruginosa in the P3 space group

Analyse Crystal structure of minor pseudopilin ternary complex of xcpvwx from the type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UTU
Type: protein
Length: 1,421 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type II secretion system protein I; Type II secretion system protein J; Type II secretion…
UniProt: Q00516, Q00517, Q00518
Ligands: CA
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 9 distinct chains · 30% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Type II secretion system protein I	protein	63	29% helix, 32% strand	Q00516
B	Type II secretion system protein J	protein	162	14% helix, 40% strand	Q00517
C	Type II secretion system protein K	protein	261	40% helix, 16% strand	Q00518
D	Type II secretion system protein I	protein	72	22% helix, 44% strand	Q00516
E	Type II secretion system protein J	protein	161	14% helix, 39% strand	Q00517
F	Type II secretion system protein K	protein	238	42% helix, 16% strand	Q00518
G	Type II secretion system protein I	protein	58	28% helix, 26% strand	Q00516
H	Type II secretion system protein J	protein	159	13% helix, 38% strand	Q00517
I	Type II secretion system protein K	protein	247	42% helix, 15% strand	Q00518

Ligands and binding sites

CA · Calcium ion · metal · 9 copies · chains C, F, I

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1044	0.76	0.78	91	empty
2	166	0.71	0.90	18	empty
3	611	0.71	0.79	78	empty
4	360	0.71	0.83	42	empty
5	528	0.70	0.80	55	empty

Interfaces

12 interfaces between chains.

B–C · 1512 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1427 Å² buried · 29 hydrogen bonds · protein-protein
H–I · 1426 Å² buried · 23 hydrogen bonds · protein-protein
D–E · 645 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 608 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6UTU · Crystal structure of minor pseudopilin ternary complex of XcpVWX from the Type 2… · the same entry in another collection · chain I against I, TM-score 1.00
Q00518 · AlphaFold monomer V2.0 prediction for type II secretion system protein K (Q00518) · a predicted model of the same protein · chain F 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 Q00516
Every structure of UniProt Q00517
Every structure of UniProt Q00518
Elsewhere: RCSB PDB 6UTU · PDBe 6UTU · UniProt Q00516 · UniProt Q00517 · UniProt Q00518

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