Research workbench
Lysx from thermus thermophilus complexed with AMP-pnp
Analyse Lysx from thermus thermophilus complexed with AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VPD
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal protein S6 modification protein
- EC
- 6.3.2.-
- UniProt
- O50144
- Ligands
- ANP, BUA
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal protein S6 modification protein (EC 6.3.2.-) | protein | 281 | 40% helix, 27% strand | O50144 |
| B | Ribosomal protein S6 modification protein (EC 6.3.2.-) | protein | 268 | 41% helix, 26% strand | O50144 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- BUA · butanoic acid · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.81 | 0.83 | 83 | CIT, ANP |
| 2 | 413 | 0.77 | 0.86 | 53 | ANP, BUA |
| 3 | 208 | 0.53 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1617 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3VPD · LysX from Thermus thermophilus complexed with AMP-PNP · 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 O50144
- Elsewhere: RCSB PDB 3VPD · PDBe 3VPD · UniProt O50144
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