Research workbench
Crystal structure of human clpp in complex with ZG111
Analyse Crystal structure of human clpp in complex with ZG111 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VP9
- Type
- protein
- Length
- 2,439 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit, mitochondrial
- EC
- 3.4.21.92
- UniProt
- Q16740
- Ligands
- 7SR, MG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 11 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 170 | 46% helix, 21% strand | Q16740 |
| C | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 168 | 46% helix, 20% strand | Q16740 |
| D | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 170 | 45% helix, 21% strand | Q16740 |
| E | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 171 | 46% helix, 21% strand | Q16740 |
| F | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 171 | 46% helix, 21% strand | Q16740 |
| H | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 180 | 43% helix, 24% strand | Q16740 |
| I | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 178 | 44% helix, 22% strand | Q16740 |
| J | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 178 | 44% helix, 24% strand | Q16740 |
| K | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 176 | 44% helix, 23% strand | Q16740 |
| L | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 179 | 44% helix, 25% strand | Q16740 |
| M, N | ATP-dependent clp protease proteolytic subunit, mitochondrial (EC 3.4.21.92) | protein | 179 | 44% helix, 25% strand | Q16740 |
Ligands and binding sites
- 7SR · (6s,9as)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-3,6, 9,9A-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide · ligand · 14 copies · chains A, G, B, C, D, E, F, H, N, I, J, K, L, M
- MG · Magnesium ion · metal · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
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 | 481 | 0.71 | 0.81 | 69 | empty |
| 2 | 251 | 0.69 | 0.84 | 26 | 7SR |
| 3 | 270 | 0.68 | 0.83 | 23 | 7SR |
| 4 | 252 | 0.67 | 0.83 | 27 | 7SR |
| 5 | 247 | 0.67 | 0.83 | 28 | 7SR |
Interfaces
28 interfaces between chains.
- H–I · 1523 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 1445 Ų buried · 12 hydrogen bonds · protein-protein
- M–N · 1415 Ų buried · 10 hydrogen bonds · protein-protein
- J–K · 1409 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1382 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7VP9 · Crystal structure of human ClpP in complex with ZG111 · the same entry in another collection · chain H against H, 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 Q16740
- Elsewhere: RCSB PDB 7VP9 · PDBe 7VP9 · UniProt Q16740
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