MolNFT v1 · #83746 · protein
Crystal structure of helicase complex 2
3WRY · Tm-1 protein: “Crystal structure of helicase complex 2”. X-ray diffraction, 3 ligands (AGS, MG, CL), 17 pockets (best druggability 0.71). MolNFT v1 #83746 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WRY
- Type
- protein
- Length
- 1,705 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tm-1 protein; Replicase large subunit
- EC
- 2.1.1.-, 2.7.7.-, 2.7.7.48, 3.6.4.13
- UniProt
- A7M6E7, P03587
- Ligands
- AGS, MG, CL
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tm-1 protein | protein | 415 | 43% helix, 19% strand | A7M6E7 |
| B | Tm-1 protein | protein | 424 | 42% helix, 19% strand | A7M6E7 |
| C | Replicase large subunit (EC 2.1.1.-, 2.7.7.-, 2.7.7.48, 3.6.4.13) | protein | 434 | 32% helix, 21% strand | P03587 |
| D | Replicase large subunit (EC 2.1.1.-, 2.7.7.-, 2.7.7.48, 3.6.4.13) | protein | 432 | 32% helix, 22% strand | P03587 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, D, B
- CL · Chloride ion · ion · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.71 | 0.81 | 60 | AGS, MG |
| 2 | 337 | 0.61 | 0.78 | 32 | empty |
| 3 | 336 | 0.60 | 0.78 | 44 | empty |
| 4 | 96 | 0.58 | 0.87 | 25 | AGS, MG |
| 5 | 129 | 0.55 | 0.83 | 22 | AGS |
Interfaces
3 interfaces between chains.
- A–B · 1846 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1079 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 959 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
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 A7M6E7
- Every structure of UniProt P03587
- Elsewhere: RCSB PDB 3WRY · PDBe 3WRY · UniProt A7M6E7 · UniProt P03587
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