MolNFT v1 · #83931 · protein
Crystal structure of archaeal pelota and GTP-bound EF1 alpha complex
3WXM · Elongation factor 1-alpha: “Crystal structure of archaeal pelota and GTP-bound EF1 alpha complex”. X-ray diffraction, 2 ligands (GTP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #83931 on GenesisL1: 3D structure, binding…
- PDB
- 3WXM
- Type
- protein
- Length
- 3,150 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 1-alpha; Protein pelota homolog
- EC
- 3.1.-.-
- UniProt
- Q9YAV0, Q9YAZ5
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor 1-alpha | protein | 432 | 22% helix, 34% strand | Q9YAV0 |
| B, D | Protein pelota homolog (EC 3.1.-.-) | protein | 357 | 38% helix, 31% strand | Q9YAZ5 |
| C | Elongation factor 1-alpha | protein | 431 | 22% helix, 35% strand | Q9YAV0 |
| E | Elongation factor 1-alpha | protein | 430 | 21% helix, 35% strand | Q9YAV0 |
| F | Protein pelota homolog (EC 3.1.-.-) | protein | 355 | 35% helix, 32% strand | Q9YAZ5 |
| G | Elongation factor 1-alpha | protein | 432 | 21% helix, 34% strand | Q9YAV0 |
| H | Protein pelota homolog (EC 3.1.-.-) | protein | 356 | 33% helix, 33% strand | Q9YAZ5 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.88 | 0.89 | 130 | empty |
| 2 | 1138 | 0.81 | 0.83 | 118 | empty |
| 3 | 664 | 0.81 | 0.86 | 89 | empty |
| 4 | 739 | 0.81 | 0.84 | 86 | empty |
| 5 | 520 | 0.80 | 0.87 | 75 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1637 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1620 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1577 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1555 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 836 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3WXM · Crystal structure of archaeal Pelota and GTP-bound EF1 alpha complex · the same entry in another collection · chain E against E, TM-score 1.00
- Q9YAV0 · AlphaFold monomer V2.0 prediction for elongation factor 1-alpha (Q9YAV0) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q9YAV0
- Every structure of UniProt Q9YAZ5
- Elsewhere: RCSB PDB 3WXM · PDBe 3WXM · UniProt Q9YAV0 · UniProt Q9YAZ5
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