Research workbench
Crystal structure of RV3378C
Analyse Crystal structure of RV3378C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CMW
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diterpene synthase
- EC
- 3.1.7.9, 3.1.7.8
- UniProt
- O50407
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diterpene synthase (EC 3.1.7.9, 3.1.7.8) | protein | 288 | 48% helix, 15% strand | O50407 |
| B | Diterpene synthase (EC 3.1.7.9, 3.1.7.8) | protein | 286 | 49% helix, 15% strand | O50407 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.82 | 0.85 | 93 | EDO, PEG |
| 2 | 614 | 0.75 | 0.82 | 65 | PEG, CIT |
| 3 | 144 | 0.43 | 0.75 | 27 | EDO |
| 4 | 142 | 0.41 | 0.74 | 27 | empty |
| 5 | 59 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3860 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 4CMW · Crystal structure of Rv3378c · 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 O50407
- Elsewhere: RCSB PDB 4CMW · PDBe 4CMW · UniProt O50407
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