Research workbench
Structure of probable translation initiation inhibitor from (RPA2473) from rhodopseudomonas palustris
Analyse Structure of probable translation initiation inhibitor from (RPA2473) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LME
- Type
- protein
- Length
- 1,542 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Possible translation initiation inhibitor
- UniProt
- Q6N6Z0
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H, J, K | Possible translation initiation inhibitor | protein | 129 | 30% helix, 30% strand | Q6N6Z0 |
| C, F | Possible translation initiation inhibitor | protein | 127 | 31% helix, 29% strand | Q6N6Z0 |
| I, L | Possible translation initiation inhibitor | protein | 128 | 31% helix, 30% strand | Q6N6Z0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E, G, F, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.83 | 0.98 | 22 | empty |
| 2 | 155 | 0.83 | 0.98 | 24 | empty |
| 3 | 150 | 0.82 | 0.97 | 23 | empty |
| 4 | 135 | 0.80 | 0.97 | 27 | empty |
| 5 | 653 | 0.76 | 0.82 | 73 | SO4 |
Interfaces
18 interfaces between chains.
- A–B · 1070 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1057 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 1054 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1053 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1050 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3LME · Structure of probable translation initiation inhibitor from (RPA2473) from… · the same entry in another collection · chain D against D, 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 Q6N6Z0
- Elsewhere: RCSB PDB 3LME · PDBe 3LME · UniProt Q6N6Z0
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