MolNFT v1 · #62499 · protein
Crystal structure of a snoal-like polyketide cyclase (ATU3018) from agrobacterium tumefaciens str. C58 at 2.12 a resolution
3EHC: “Crystal structure of a snoal-like polyketide cyclase (ATU3018) from agrobacterium tumefaciens str. C58 at…”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.67). MolNFT v1 #62499 on GenesisL1: 3D structure, binding…
- PDB
- 3EHC
- Type
- protein
- Length
- 507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snoal-like polyketide cyclase
- UniProt
- Q7CRD4
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Snoal-like polyketide cyclase | protein | 127 | 33% helix, 39% strand | Q7CRD4 |
| B | Snoal-like polyketide cyclase | protein | 128 | 33% helix, 38% strand | Q7CRD4 |
| D | Snoal-like polyketide cyclase | protein | 125 | 34% helix, 39% strand | Q7CRD4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.67 | 0.81 | 41 | SO4 |
| 2 | 357 | 0.66 | 0.80 | 45 | empty |
| 3 | 345 | 0.66 | 0.80 | 41 | SO4 |
| 4 | 341 | 0.65 | 0.80 | 46 | empty |
| 5 | 472 | 0.60 | 0.75 | 50 | empty |
Interfaces
4 interfaces between chains.
- A–B · 977 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 962 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 227 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 126 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 3EHC · Crystal structure of a snoal-like polyketide cyclase (atu3018) from agrobacterium… · 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 Q7CRD4
- Elsewhere: RCSB PDB 3EHC · PDBe 3EHC · UniProt Q7CRD4
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