Research workbench
Complex structure of human elongation factor 1B gamma GST-liked domain and delta N-terminal domain
Analyse Complex structure of human elongation factor 1B gamma GST-liked domain and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JPO
- Type
- protein
- Length
- 885 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 1-gamma; Elongation factor 1-delta
- UniProt
- P26641, P29692
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor 1-gamma | protein | 216 | 56% helix, 8% strand | P26641 |
| B | Elongation factor 1-gamma | protein | 215 | 57% helix, 8% strand | P26641 |
| C | Elongation factor 1-gamma | protein | 207 | 59% helix, 8% strand | P26641 |
| D | Elongation factor 1-gamma | protein | 215 | 55% helix, 11% strand | P26641 |
| E | Elongation factor 1-delta | protein | 32 | 72% helix, 0% strand | P29692 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.85 | 0.88 | 88 | empty |
| 2 | 1084 | 0.82 | 0.83 | 140 | empty |
| 3 | 72 | 0.66 | 0.92 | 22 | GOL |
| 4 | 78 | 0.42 | 0.79 | 20 | empty |
| 5 | 59 | 0.38 | 0.80 | 15 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1235 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1226 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 790 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 732 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 667 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5JPO · Complex structure of human elongation factor 1B gamma GST-liked domain and delta… · the same entry in another collection · chain E against E, TM-score 1.00
- P26641 · AlphaFold monomer V2.0 prediction for elongation factor 1-gamma (P26641) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P29692 · AlphaFold monomer V2.0 prediction for elongation factor 1-delta (P29692) · a predicted model of the same protein · chain E against A, TM-score 0.65
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 P26641
- Every structure of UniProt P29692
- Elsewhere: RCSB PDB 5JPO · PDBe 5JPO · UniProt P26641 · UniProt P29692
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