MolNFT v1 · #57385 · protein
Crystal structure of escherichia COLI genx in complex with elongation factor P
3A5Z · Putative lysyl-tRNA synthetase: “Crystal structure of escherichia COLI genx in complex with elongation factor P”. X-ray diffraction, 1 ligand (KAA), 20 pockets (best druggability 0.83). MolNFT v1 #57385 on GenesisL1: 3D structure…
- PDB
- 3A5Z
- Type
- protein
- Length
- 1,836 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lysyl-tRNA synthetase; Elongation factor P
- EC
- 6.1.1.6
- UniProt
- C3SGA2, C3SGD7
- Ligands
- KAA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Putative lysyl-tRNA synthetase (EC 6.1.1.6) | protein | 323 | 41% helix, 21% strand | C3SGA2 |
| B | Elongation factor P | protein | 134 | 5% helix, 50% strand | C3SGD7 |
| C | Putative lysyl-tRNA synthetase (EC 6.1.1.6) | protein | 324 | 39% helix, 21% strand | C3SGA2 |
| D, H | Elongation factor P | protein | 175 | 6% helix, 53% strand | C3SGD7 |
| F | Elongation factor P | protein | 59 | 0% helix, 53% strand | C3SGD7 |
| G | Putative lysyl-tRNA synthetase (EC 6.1.1.6) | protein | 323 | 37% helix, 21% strand | C3SGA2 |
Ligands and binding sites
- KAA · 5'-O-[(L-lysylamino)sulfonyl]adenosine · ligand · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.83 | 0.91 | 63 | KAA |
| 2 | 346 | 0.82 | 0.92 | 62 | KAA |
| 3 | 410 | 0.82 | 0.91 | 63 | KAA |
| 4 | 452 | 0.82 | 0.90 | 66 | KAA |
| 5 | 695 | 0.81 | 0.85 | 86 | empty |
Interfaces
13 interfaces between chains.
- E–G · 2548 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 2531 Ų buried · 50 hydrogen bonds · protein-protein
- G–H · 1043 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1001 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 992 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3A5Z · Crystal structure of Escherichia coli GenX in complex with elongation factor P · 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 C3SGA2
- Every structure of UniProt C3SGD7
- Elsewhere: RCSB PDB 3A5Z · PDBe 3A5Z · UniProt C3SGA2 · UniProt C3SGD7
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