MolNFT v1 · #103287 · protein
Elongation factor TU:TS complex with bound gdpnp
4PC6: “Elongation factor TU:TS complex with bound gdpnp”. X-ray diffraction, 1 ligand (GNP), 18 pockets (best druggability 0.78). MolNFT v1 #103287 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PC6
- Type
- protein
- Length
- 1,286 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor tu; Elongation factor ts
- UniProt
- B1X6I9, C9QRL8
- Ligands
- GNP
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor tu | protein | 363 | 23% helix, 39% strand | B1X6I9 |
| C | Elongation factor ts | protein | 277 | 52% helix, 22% strand | C9QRL8 |
| B | Elongation factor tu | protein | 368 | 23% helix, 37% strand | B1X6I9 |
| D | Elongation factor ts | protein | 278 | 53% helix, 22% strand | C9QRL8 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B, D
- GOL · Glycerol · additive · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.78 | 0.87 | 59 | GOL |
| 2 | 379 | 0.72 | 0.83 | 54 | GOL |
| 3 | 279 | 0.59 | 0.78 | 34 | empty |
| 4 | 242 | 0.58 | 0.79 | 36 | empty |
| 5 | 167 | 0.51 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1840 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1828 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1222 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 402 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 162 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4PC6 · Elongation factor Tu:Ts complex with bound GDPNP · the same entry in another collection · chain A against A, TM-score 1.00
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 B1X6I9
- Every structure of UniProt C9QRL8
- Elsewhere: RCSB PDB 4PC6 · PDBe 4PC6 · UniProt B1X6I9 · UniProt C9QRL8
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