MolNFT v1 · #114648 · protein

The crystal structure of minor pseudopilin binary complex of xcpv and xcpw from the type 2 secretion system of pseudomonas aeruginosa

5BW0 · Type II secretion system protein J: “The crystal structure of minor pseudopilin binary complex of xcpv and xcpw from the type 2 secretion system…”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.83). MolNFT v1…

PDB: 5BW0
Type: protein
Length: 978 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type II secretion system protein J; Type II secretion system protein I
UniProt: Q00517, Q00516
Ligands: SO4
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 22% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Type II secretion system protein J	protein	152	18% helix, 45% strand	Q00517
B	Type II secretion system protein I	protein	89	30% helix, 42% strand	Q00516
C	Type II secretion system protein J	protein	159	13% helix, 43% strand	Q00517
D	Type II secretion system protein I	protein	84	31% helix, 43% strand	Q00516
E	Type II secretion system protein J	protein	163	20% helix, 42% strand	Q00517
F	Type II secretion system protein I	protein	91	32% helix, 40% strand	Q00516
G	Type II secretion system protein J	protein	159	14% helix, 43% strand	Q00517
H	Type II secretion system protein I	protein	81	32% helix, 37% strand	Q00516

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, F, C

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1148	0.83	0.84	86	SO4
2	307	0.55	0.76	29	empty
3	158	0.40	0.73	24	empty
4	93	0.37	0.75	15	empty
5	55	0.35	0.78	14	empty

Interfaces

12 interfaces between chains.

E–F · 962 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 873 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 865 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 847 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 477 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5BW0 · The crystal structure of minor pseudopilin binary complex of XcpV and XcpW from the Type… · the same entry in another collection · chain H against H, TM-score 1.00
Q00516 · AlphaFold monomer V2.0 prediction for type II secretion system protein I (Q00516) · a predicted model of the same protein · chain F against A, TM-score 0.98

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 Q00517
Every structure of UniProt Q00516
Elsewhere: RCSB PDB 5BW0 · PDBe 5BW0 · UniProt Q00517 · UniProt Q00516

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