Research workbench
E. COLI P pilus chaperone-subunit complex papd-paph bound to pilus biogenesis inhibitor, pilicide 2C
Analyse E. COLI P pilus chaperone-subunit complex papd-paph bound to pilus biogenesis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XG4
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein papd; Pap fimbrial minor pilin protein
- UniProt
- P15319, P07111
- Ligands
- XC2, CO
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein papd | protein | 216 | 8% helix, 51% strand | P15319 |
| B | Pap fimbrial minor pilin protein | protein | 149 | 3% helix, 40% strand | P07111 |
Ligands and binding sites
- XC2 · (3R)-8-cyclopropyl-6-(morpholin-4-ylmethyl)-7-(1-naphthylmethyl)-5-oxo-2,3-dihydro-5H-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid · ligand · chains A
- CO · Cobalt (II) ion · metal · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.45 | 0.77 | 21 | empty |
| 2 | 56 | 0.31 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2022 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2XG4 · E. coli P pilus chaperone-subunit complex PapD-PapH bound to pilus biogenesis inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P15319 · AlphaFold monomer V2.0 prediction for chaperone protein papd (P15319) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P07111 · AlphaFold monomer V2.0 prediction for pap fimbrial minor pilin protein (P07111) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P15319
- Every structure of UniProt P07111
- Elsewhere: RCSB PDB 2XG4 · PDBe 2XG4 · UniProt P15319 · UniProt P07111
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