MolNFT v1 · #118000 · protein

Pseudomonas aeruginosa pilm bound to ADP

5EOX · Type 4 fimbrial biogenesis protein pilm: “Pseudomonas aeruginosa pilm bound to ADP”. X-ray diffraction, 2 ligands (ADP, MG), 5 pockets (best druggability 0.77). MolNFT v1 #118000 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5EOX
Type: protein
Length: 704 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type 4 fimbrial biogenesis protein pilm
UniProt: G3XD28
Ligands: ADP, MG
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Type 4 fimbrial biogenesis protein pilm	protein	351	40% helix, 30% strand	G3XD28
B	Type 4 fimbrial biogenesis protein pilm	protein	353	42% helix, 29% strand	G3XD28

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	757	0.77	0.81	85	ADP, MG
2	662	0.72	0.79	70	ADP, MG
3	544	0.67	0.77	56	empty
4	277	0.57	0.78	34	empty
5	62	0.31	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 1649 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5EOX · Pseudomonas aeruginosa PilM bound to ADP · the same entry in another collection · chain B against B, TM-score 1.00
G3XD28 · AlphaFold monomer V2.0 prediction for type IV pilus inner membrane component pilm (G3XD28) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 G3XD28
Elsewhere: RCSB PDB 5EOX · PDBe 5EOX · UniProt G3XD28

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