MolNFT v1 · #94703 · protein
Crystal structure of nucleotide-bound W-W-W clpx hexamer
4I4L · ATP-dependent clp protease ATP-binding subunit clpx: “Crystal structure of nucleotide-bound W-W-W clpx hexamer”. X-ray diffraction, 2 ligands (ADP, SO4), 15 pockets (best druggability 0.84). MolNFT v1 #94703 on GenesisL1: 3D…
- PDB
- 4I4L
- Type
- protein
- Length
- 1,814 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpx
- UniProt
- P0A6H1
- Ligands
- ADP, SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease ATP-binding subunit clpx | protein | 299 | 49% helix, 11% strand | P0A6H1 |
| B | ATP-dependent clp protease ATP-binding subunit clpx | protein | 305 | 50% helix, 11% strand | P0A6H1 |
| C | ATP-dependent clp protease ATP-binding subunit clpx | protein | 305 | 50% helix, 11% strand | P0A6H1 |
| D | ATP-dependent clp protease ATP-binding subunit clpx | protein | 309 | 47% helix, 11% strand | P0A6H1 |
| E | ATP-dependent clp protease ATP-binding subunit clpx | protein | 294 | 46% helix, 11% strand | P0A6H1 |
| F | ATP-dependent clp protease ATP-binding subunit clpx | protein | 302 | 45% helix, 11% strand | P0A6H1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.84 | 0.85 | 95 | SO4 |
| 2 | 1037 | 0.84 | 0.85 | 95 | SO4 |
| 3 | 1008 | 0.83 | 0.84 | 94 | ADP |
| 4 | 998 | 0.82 | 0.83 | 117 | SO4 |
| 5 | 1127 | 0.79 | 0.81 | 110 | SO4 |
Interfaces
7 interfaces between chains.
- A–B · 1418 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1412 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1380 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1136 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1054 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4I4L · Crystal Structure of Nucleotide-Bound W-W-W ClpX Hexamer · the same entry in another collection · chain D against D, TM-score 1.00
- P0A6H1 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease ATP- binding subunit… · a predicted model of the same protein · chain B 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 P0A6H1
- Elsewhere: RCSB PDB 4I4L · PDBe 4I4L · UniProt P0A6H1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.