MolNFT v1 · #117148 · protein
Crystal structure of the active form of the proteolytic complex CLPP1 and CLPP2
5DZK · ATP-dependent clp protease proteolytic subunit 2: “Crystal structure of the active form of the proteolytic complex CLPP1 and CLPP2”. X-ray diffraction, 1 ligand (BEZ), 20 pockets (best druggability 0.75). MolNFT v1 #117148 on…
- PDB
- 5DZK
- Type
- protein
- Length
- 5,310 residues
- Chains
- 56
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit 2; Bez-leu-leu; ATP-dependent clp protease…
- EC
- 3.4.21.92
- UniProt
- P9WPC2, P9WPC4
- Ligands
- BEZ
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, d, f, g | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 196 | 43% helix, 24% strand | P9WPC2 |
| O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, o, p, q, r, s, t, u, v, w, x, y, z, 3, 4 | Bez-leu-leu | protein | 2 | 0% helix, 0% strand | — |
| B, E, b, e | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 200 | 42% helix, 24% strand | P9WPC2 |
| G | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 195 | 43% helix, 26% strand | P9WPC2 |
| H, I, J, K, L, M, h, i, j, k, l, m, n | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 178 | 49% helix, 23% strand | P9WPC4 |
| N | ATP-dependent clp protease proteolytic subunit 1 (EC 3.4.21.92) | protein | 179 | 49% helix, 24% strand | P9WPC4 |
| a, c | ATP-dependent clp protease proteolytic subunit 2 (EC 3.4.21.92) | protein | 197 | 42% helix, 26% strand | P9WPC2 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 28 copies · chains A, O, B, P, C, Q, D, R, E, S, F, T, G, U, H, V, I, W, J, X, K, Y, L, Z, M, 1, N, 2, a, o, b, p, c, q, d, r, e, s, f, t, g, u, h, v, n, i, w, j, x, k, y, l, z, m, 3, 4
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 | 1001 | 0.75 | 0.78 | 85 | empty |
| 2 | 916 | 0.72 | 0.77 | 84 | BEZ |
| 3 | 906 | 0.72 | 0.77 | 88 | BEZ |
| 4 | 870 | 0.72 | 0.77 | 82 | BEZ |
| 5 | 928 | 0.72 | 0.76 | 90 | BEZ |
Interfaces
127 interfaces between chains.
- A–G · 1859 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1850 Ų buried · 28 hydrogen bonds · protein-protein
- a–g · 1840 Ų buried · 29 hydrogen bonds · protein-protein
- c–d · 1839 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1838 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 covalent, 1 isopeptide (covalent ligand, isopeptide).
Compared structures
- 5DZK · Crystal structure of the active form of the proteolytic complex clpP1 and clpP2 · the same entry in another collection · chain I against I, 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 P9WPC2
- Every structure of UniProt P9WPC4
- Elsewhere: RCSB PDB 5DZK · PDBe 5DZK · UniProt P9WPC2 · UniProt P9WPC4
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