Research workbench
Crystal structure of RV3378C with MG2+ and ppi
Analyse Crystal structure of RV3378C with MG2+ and ppi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WQL
- Type
- protein
- Length
- 1,139 residues
- Chains
- 4
- 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
- Ligands
- MG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diterpene synthase (EC 3.1.7.9, 3.1.7.8) | protein | 283 | 49% helix, 14% strand | O50407 |
| B | Diterpene synthase (EC 3.1.7.9, 3.1.7.8) | protein | 286 | 50% helix, 15% strand | O50407 |
| C | Diterpene synthase (EC 3.1.7.9, 3.1.7.8) | protein | 286 | 49% helix, 15% strand | O50407 |
| D | Diterpene synthase (EC 3.1.7.9, 3.1.7.8) | protein | 284 | 49% helix, 15% strand | O50407 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.84 | 0.85 | 99 | MG |
| 2 | 966 | 0.83 | 0.84 | 102 | MG |
| 3 | 551 | 0.75 | 0.82 | 53 | MG |
| 4 | 443 | 0.71 | 0.81 | 58 | MG |
| 5 | 132 | 0.48 | 0.79 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3843 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3726 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 446 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 418 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 282 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3WQL · Crystal structure of Rv3378c with Mg2+ and PPi · 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 3WQL · PDBe 3WQL · UniProt O50407
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.