Research workbench
Elongator catalytic subcomplex ELP123 lobe
Analyse Elongator catalytic subcomplex ELP123 lobe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QK7
- Type
- protein
- Length
- 2,592 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongator complex protein 1; Elongator complex protein 2; Elongator complex protein 3
- EC
- 2.3.1.48
- UniProt
- Q06706, P42935, Q02908
- Ligands
- SF4, 5AD
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongator complex protein 1 | protein | 1161 | 29% helix, 25% strand | Q06706 |
| B | Elongator complex protein 2 | protein | 749 | 3% helix, 46% strand | P42935 |
| C | Elongator complex protein 3 (EC 2.3.1.48) | protein | 444 | 32% helix, 22% strand | Q02908 |
| D | Elongator complex protein 1 | protein | 238 | 75% helix, 0% strand | Q06706 |
Ligands and binding sites
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 | 1037 | 0.83 | 0.84 | 92 | SF4, 5AD |
| 2 | 1058 | 0.81 | 0.82 | 121 | empty |
| 3 | 1076 | 0.81 | 0.82 | 98 | empty |
| 4 | 990 | 0.78 | 0.80 | 61 | empty |
| 5 | 128 | 0.77 | 0.96 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2458 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1817 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1432 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 350 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6QK7 · Elongator catalytic subcomplex Elp123 lobe · the same entry in another collection · chain D against D, TM-score 1.00
- P42935 · AlphaFold monomer V2.0 prediction for elongator complex protein 2 (P42935) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q02908 · AlphaFold monomer V2.0 prediction for elongator complex protein 3 (Q02908) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q06706 · AlphaFold monomer V2.0 prediction for elongator complex protein 1 (Q06706) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q06706
- Every structure of UniProt P42935
- Every structure of UniProt Q02908
- Elsewhere: RCSB PDB 6QK7 · PDBe 6QK7 · UniProt Q06706 · UniProt P42935 · UniProt Q02908
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