MolNFT v1 · #83357 · protein
TRNA processing enzyme (apo form 2)
3WFP · Poly a polymerase: “TRNA processing enzyme (apo form 2)”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #83357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WFP
- Type
- protein
- Length
- 3,387 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly a polymerase
- EC
- 2.7.7.72
- UniProt
- O67911
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly a polymerase (EC 2.7.7.72) | protein | 455 | 57% helix, 10% strand | O67911 |
| B | Poly a polymerase (EC 2.7.7.72) | protein | 450 | 59% helix, 10% strand | O67911 |
| C, D | Poly a polymerase (EC 2.7.7.72) | protein | 419 | 55% helix, 11% strand | O67911 |
| E, F, G, H | Poly a polymerase (EC 2.7.7.72) | protein | 411 | 57% helix, 12% strand | O67911 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.81 | 0.83 | 70 | SO4 |
| 2 | 971 | 0.81 | 0.82 | 67 | SO4 |
| 3 | 750 | 0.77 | 0.82 | 70 | SO4 |
| 4 | 737 | 0.77 | 0.82 | 75 | SO4 |
| 5 | 1110 | 0.76 | 0.79 | 78 | SO4 |
Interfaces
11 interfaces between chains.
- A–B · 2351 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2292 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2285 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2264 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 479 Ų buried · 3 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 O67911
- Elsewhere: RCSB PDB 3WFP · PDBe 3WFP · UniProt O67911
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