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Crystal structure of the P pilus rod subunit papa

Analyse Crystal structure of the P pilus rod subunit papa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2UY7
Type: protein
Length: 1,484 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmid chaperone papd protein; Pap fimbrial major pilin protein
UniProt: Q1R2W9, P04127
Ligands: SO4
Pockets: 11 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Periplasmid chaperone papd protein	protein	216	8% helix, 51% strand	Q1R2W9
B, F	Pap fimbrial major pilin protein	protein	156	3% helix, 37% strand	P04127
D, H	Pap fimbrial major pilin protein	protein	154	5% helix, 33% strand	P04127

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains A, C, E, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	276	0.66	0.82	31	empty
2	254	0.63	0.81	27	empty
3	232	0.60	0.80	28	empty
4	306	0.60	0.78	26	empty
5	83	0.60	0.88	20	empty

Interfaces

4 interfaces between chains.

G–H · 2149 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 2098 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 2083 Å² buried · 49 hydrogen bonds · protein-protein
E–F · 2025 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2UY7 · Crystal structure of the P pilus rod subunit PapA · the same entry in another collection · chain H against H, TM-score 1.00
P04127 · AlphaFold monomer V2.0 prediction for pap fimbrial major pilin protein (P04127) · a predicted model of the same protein · chain B against A, TM-score 0.74

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 Q1R2W9
Every structure of UniProt P04127
Elsewhere: RCSB PDB 2UY7 · PDBe 2UY7 · UniProt Q1R2W9 · UniProt P04127

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