Research workbench
Clpxp from neisseria meningitidis - conformation B
Analyse Clpxp from neisseria meningitidis - conformation B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VFX
- Type
- protein
- Length
- 4,689 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clpx; Unidentified peptide substrate…
- EC
- 3.4.21.92
- UniProt
- A0A0Y4ZJG4, A0A0Y5K536
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 12 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | ATP-dependent clp protease ATP-binding subunit clpx | protein | 333 | 44% helix, 14% strand | A0A0Y4ZJG4 |
| B | ATP-dependent clp protease ATP-binding subunit clpx | protein | 337 | 42% helix, 14% strand | A0A0Y4ZJG4 |
| E | ATP-dependent clp protease ATP-binding subunit clpx | protein | 341 | 42% helix, 13% strand | A0A0Y4ZJG4 |
| F | ATP-dependent clp protease ATP-binding subunit clpx | protein | 321 | 46% helix, 13% strand | A0A0Y4ZJG4 |
| D | ATP-dependent clp protease ATP-binding subunit clpx | protein | 339 | 43% helix, 13% strand | A0A0Y4ZJG4 |
| A | ATP-dependent clp protease ATP-binding subunit clpx | protein | 340 | 44% helix, 13% strand | A0A0Y4ZJG4 |
| G | Unidentified peptide substrate | protein | 7 | 0% helix, 0% strand | — |
| L, O, P, Q, R, S, T, U, J, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 191 | 44% helix, 24% strand | A0A0Y5K536 |
| H | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 190 | 44% helix, 23% strand | A0A0Y5K536 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 44% helix, 24% strand | A0A0Y5K536 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 193 | 44% helix, 25% strand | A0A0Y5K536 |
| M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 186 | 45% helix, 22% strand | A0A0Y5K536 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains C, D, B, E, F, A
- ADP · Adenosine-5'-diphosphate · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains C, D, B, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.85 | 0.88 | 91 | ATP, MG |
| 2 | 554 | 0.83 | 0.89 | 50 | ATP, MG |
| 3 | 628 | 0.82 | 0.87 | 60 | ATP, MG |
| 4 | 570 | 0.82 | 0.88 | 56 | ATP, MG |
| 5 | 398 | 0.79 | 0.88 | 53 | empty |
Interfaces
63 interfaces between chains.
- E–D · 2317 Ų buried · 25 hydrogen bonds · protein-protein
- B–A · 2210 Ų buried · 29 hydrogen bonds · protein-protein
- C–B · 2133 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2080 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1753 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6VFX · ClpXP from Neisseria meningitidis - Conformation B · the same entry in another collection · chain C against C, 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 A0A0Y4ZJG4
- Every structure of UniProt A0A0Y5K536
- Elsewhere: RCSB PDB 6VFX · PDBe 6VFX · UniProt A0A0Y4ZJG4 · UniProt A0A0Y5K536
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