MolNFT v1 · #51122 · protein

Crystal structure of the P pilus rod subunit papa

2UY6 · Periplasmid chaperone papd protein: “Crystal structure of the P pilus rod subunit papa”. X-ray diffraction, 6 pockets (best druggability 0.54). MolNFT v1 #51122 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2UY6
Type: protein
Length: 510 residues
Chains: 3
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
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Periplasmid chaperone papd protein	protein	216	8% helix, 50% strand	Q1R2W9
B	Pap fimbrial major pilin protein	protein	150	4% helix, 47% strand	P04127
C	Pap fimbrial major pilin protein	protein	144	6% helix, 52% strand	P04127

Pockets

6 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	246	0.54	0.77	24	empty
2	144	0.51	0.79	32	empty
3	201	0.50	0.77	24	empty
4	91	0.43	0.79	18	empty
5	67	0.28	0.73	19	empty

Interfaces

3 interfaces between chains.

A–B · 1789 Å² buried · 35 hydrogen bonds · protein-protein
B–C · 1020 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 249 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

2UY6 · Crystal structure of the P pilus rod subunit PapA · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.95

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 2UY6 · PDBe 2UY6 · UniProt Q1R2W9 · UniProt P04127

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