Research workbench
Crystal structure analysis of the translation factor RF3
Analyse Crystal structure analysis of the translation factor RF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VQT
- Type
- protein
- Length
- 1,970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide chain release factor 3
- UniProt
- B8DIL5
- Ligands
- GDP
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide chain release factor 3 | protein | 495 | 32% helix, 30% strand | B8DIL5 |
| B | Peptide chain release factor 3 | protein | 490 | 33% helix, 30% strand | B8DIL5 |
| C | Peptide chain release factor 3 | protein | 491 | 32% helix, 30% strand | B8DIL5 |
| D | Peptide chain release factor 3 | protein | 494 | 31% helix, 31% strand | B8DIL5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.69 | 0.81 | 56 | empty |
| 2 | 314 | 0.67 | 0.82 | 41 | empty |
| 3 | 309 | 0.67 | 0.82 | 43 | empty |
| 4 | 87 | 0.65 | 0.91 | 19 | empty |
| 5 | 513 | 0.64 | 0.76 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1071 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 36 Ų buried · 0 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 B8DIL5
- Elsewhere: RCSB PDB 3VQT · PDBe 3VQT · UniProt B8DIL5
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