Research workbench
CLPP1P2 complex from M. tuberculosis with glf-cmk bound to CLPP1
Analyse CLPP1P2 complex from M. tuberculosis with glf-cmk bound to CLPP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VGQ
- Type
- protein
- Length
- 2,527 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit 1; ATP-dependent clp protease proteolytic…
- EC
- 3.4.21.92
- UniProt
- P9WPC5, A0A045HBE0
- Ligands
- 0QE
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 3 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N, H, I, J, K, L, M | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 178 | 49% helix, 23% strand | P9WPC5 |
| A, B, C, D, E, F, G | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 46% helix, 23% strand | A0A045HBE0 |
| U, O, P, Q, R, S, T | Z-gly-leu-phe-CH2CL | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 0QE · Chloromethane · ion · 7 copies · chains N, U, H, O, I, P, J, Q, K, R, L, S, M, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.74 | 0.79 | 124 | empty |
| 2 | 864 | 0.71 | 0.76 | 92 | empty |
| 3 | 584 | 0.71 | 0.79 | 90 | empty |
| 4 | 578 | 0.70 | 0.79 | 91 | empty |
| 5 | 525 | 0.69 | 0.79 | 76 | empty |
Interfaces
49 interfaces between chains.
- B–C · 1474 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1470 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 1470 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1468 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1466 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6VGQ · ClpP1P2 complex from M. tuberculosis with GLF-CMK bound to ClpP1 · 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 P9WPC5
- Every structure of UniProt A0A045HBE0
- Elsewhere: RCSB PDB 6VGQ · PDBe 6VGQ · UniProt P9WPC5 · UniProt A0A045HBE0
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