Research workbench
Crystal structure of secreted protein cofj from etec.
Analyse Crystal structure of secreted protein cofj from etec. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YQ0
- Type
- protein
- Length
- 2,411 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cofj
- UniProt
- Q93I65
- Ligands
- CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | Cofj | protein | 301 | 12% helix, 43% strand | Q93I65 |
| C | Cofj | protein | 304 | 13% helix, 42% strand | Q93I65 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.80 | 0.82 | 113 | empty |
| 2 | 1042 | 0.80 | 0.82 | 110 | CA |
| 3 | 415 | 0.75 | 0.85 | 67 | empty |
| 4 | 1083 | 0.72 | 0.76 | 91 | empty |
| 5 | 939 | 0.72 | 0.76 | 97 | empty |
Interfaces
15 interfaces between chains.
- B–D · 1429 Ų buried · 21 hydrogen bonds · protein-protein
- E–H · 1415 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1410 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1339 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 484 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5YQ0 · Crystal structure of secreted protein CofJ from ETEC. · the same entry in another collection · chain A against A, TM-score 1.00
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 Q93I65
- Elsewhere: RCSB PDB 5YQ0 · PDBe 5YQ0 · UniProt Q93I65
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