MolNFT v1 · #118042 · protein

Pseudomonas aeruginosa pilm bound to AMP-pnp

5EQ6 · Type 4 fimbrial biogenesis protein pilm: “Pseudomonas aeruginosa pilm bound to AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 5 pockets (best druggability 0.77). MolNFT v1 #118042 on GenesisL1: 3D structure, binding sites and…

PDB: 5EQ6
Type: protein
Length: 709 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: ANP, MG
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Type 4 fimbrial biogenesis protein pilm	protein	357	38% helix, 29% strand	G3XD28
B	Type 4 fimbrial biogenesis protein pilm	protein	352	41% helix, 29% strand	G3XD28

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	784	0.77	0.81	74	ANP, MG
2	642	0.74	0.80	68	ANP, MG
3	853	0.70	0.76	86	empty
4	75	0.37	0.77	18	empty
5	50	0.28	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 1513 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5EQ6 · Pseudomonas aeruginosa PilM bound to AMP-PNP · the same entry in another collection · chain A against A, 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 5EQ6 · PDBe 5EQ6 · UniProt G3XD28

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