MolNFT v1 · #159525 · protein
Crystal structure of cymd prenyltransferase complexed with L- tryptophan
6OS5: “Crystal structure of cymd prenyltransferase complexed with L- tryptophan”. X-ray diffraction, 3 ligands (TRP, DPO, BEZ), 13 pockets (best druggability 0.79). MolNFT v1 #159525 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6OS5
- Type
- protein
- Length
- 1,049 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cymd prenyltransferase
- UniProt
- A8M6W6
- Ligands
- TRP, DPO, BEZ
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cymd prenyltransferase | protein | 353 | 37% helix, 20% strand | A8M6W6 |
| B | Cymd prenyltransferase | protein | 354 | 38% helix, 20% strand | A8M6W6 |
| C | Cymd prenyltransferase | protein | 342 | 40% helix, 20% strand | A8M6W6 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- DPO · Diphosphate · ligand · 2 copies · chains B, C
- BEZ · Benzoic acid · ligand · chains A
- IMD · Imidazole · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.79 | 0.87 | 63 | TRP, BEZ |
| 2 | 1002 | 0.74 | 0.77 | 95 | empty |
| 3 | 427 | 0.73 | 0.83 | 71 | TRP, DPO, IMD |
| 4 | 171 | 0.73 | 0.90 | 24 | DPO |
| 5 | 316 | 0.59 | 0.77 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–C · 493 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 400 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 328 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6OS5 · Crystal structure of CymD prenyltransferase complexed with L-tryptophan · 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 A8M6W6
- Elsewhere: RCSB PDB 6OS5 · PDBe 6OS5 · UniProt A8M6W6
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