MolNFT v1 · #120664 · protein
Complex of elongation factor 2-50S ribosomal protein L12
5H7L: “Complex of elongation factor 2-50S ribosomal protein L12”. X-ray diffraction, 1 ligand (GCP), 17 pockets (best druggability 0.82). MolNFT v1 #120664 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H7L
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 2; 50S ribosomal protein L12
- UniProt
- O59521, O57705
- Ligands
- GCP
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor 2 | protein | 694 | 36% helix, 27% strand | O59521 |
| B | Elongation factor 2 | protein | 691 | 36% helix, 26% strand | O59521 |
| G | 50S ribosomal protein L12 | protein | 10 | 40% helix, 0% strand | O57705 |
| E | 50S ribosomal protein L12 | protein | 9 | 44% helix, 0% strand | O57705 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.82 | 0.83 | 97 | empty |
| 2 | 836 | 0.75 | 0.79 | 69 | empty |
| 3 | 64 | 0.60 | 0.90 | 21 | empty |
| 4 | 126 | 0.58 | 0.84 | 30 | empty |
| 5 | 59 | 0.52 | 0.87 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 713 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 568 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 553 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5H7L · Complex of Elongation factor 2-50S ribosomal protein L12 · the same entry in another collection · chain E against E, TM-score 1.00
- O59521 · AlphaFold monomer V2.0 prediction for elongation factor 2 (O59521) · a predicted model of the same protein · chain B against A, TM-score 0.63
- O57705 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L12 (O57705) · a predicted model of the same protein · chain E against A, TM-score 0.57
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 O59521
- Every structure of UniProt O57705
- Elsewhere: RCSB PDB 5H7L · PDBe 5H7L · UniProt O59521 · UniProt O57705
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