Research workbench
Leca from pseudomonas aeruginosa in complex with a catechol CAS no. 61445-50-9
Analyse Leca from pseudomonas aeruginosa in complex with a catechol CAS no. 61445-50-9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YOH
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pa-I galactophilic lectin
- UniProt
- Q05097
- Ligands
- P4H, CA
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pa-I galactophilic lectin | protein | 121 | 0% helix, 45% strand | Q05097 |
Ligands and binding sites
- P4H · [2,4-bis(oxidanyl)phenyl]-[3,4-bis(oxidanyl) phenyl]methanone · ligand · 3 copies · chains A, B, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.63 | 0.93 | 24 | empty |
| 2 | 80 | 0.62 | 0.90 | 24 | empty |
| 3 | 61 | 0.26 | 0.72 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1068 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1054 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 249 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6YOH · LecA from Pseudomonas aeruginosa in complex with a catechol CAS no. 61445-50-9 · the same entry in another collection · chain A against A, TM-score 1.00
- Q05097 · AlphaFold monomer V2.0 prediction for pa-I galactophilic lectin (Q05097) · a predicted model of the same protein · chain A 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 Q05097
- Elsewhere: RCSB PDB 6YOH · PDBe 6YOH · UniProt Q05097
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