MolNFT v1 · #66793 · protein
Crystal structure of a putative polyketide cyclase (XCC0381) from xanthomonas campestris pv. campestris at 1.50 a resolution
3I0Y: “Crystal structure of a putative polyketide cyclase (XCC0381) from xanthomonas campestris pv. campestris at…”. X-ray diffraction, 2 ligands (UNL, CL), 9 pockets (best druggability 0.77). MolNFT v1 #66793 on GenesisL1: 3D structure…
- PDB
- 3I0Y
- Type
- protein
- Length
- 545 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative polyketide cyclase
- UniProt
- Q8PDF7
- Ligands
- UNL, CL
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative polyketide cyclase | protein | 138 | 35% helix, 42% strand | Q8PDF7 |
| B | Putative polyketide cyclase | protein | 135 | 34% helix, 43% strand | Q8PDF7 |
| C | Putative polyketide cyclase | protein | 136 | 35% helix, 43% strand | Q8PDF7 |
| D | Putative polyketide cyclase | protein | 136 | 34% helix, 43% strand | Q8PDF7 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.77 | 0.88 | 37 | CL, UNL |
| 2 | 354 | 0.77 | 0.87 | 44 | CL, UNL |
| 3 | 276 | 0.75 | 0.88 | 44 | CL, UNL |
| 4 | 294 | 0.71 | 0.84 | 34 | CL, UNL |
| 5 | 235 | 0.67 | 0.84 | 47 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1037 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1022 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 718 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3I0Y · Crystal structure of a putative polyketide cyclase (xcc0381) from xanthomonas campestris… · 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 Q8PDF7
- Elsewhere: RCSB PDB 3I0Y · PDBe 3I0Y · UniProt Q8PDF7
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