MolNFT v1 · #116669 · protein
Crystal structure of N. meningitidis clpp in complex with agonist adep A54556.
5DKP · ATP-dependent clp protease proteolytic subunit: “Crystal structure of N. meningitidis clpp in complex with agonist adep A54556.”. X-ray diffraction, 3 ligands (OTT, K, NA), 20 pockets (best druggability 0.78). MolNFT v1 #116669 on…
- PDB
- 5DKP
- Type
- protein
- Length
- 5,496 residues
- Chains
- 56
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; Agonist adep A54556
- EC
- 3.4.21.92
- UniProt
- Q9JZ38
- Ligands
- OTT, K, NA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 15 distinct chains · 44% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, m | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 190 | 44% helix, 25% strand | Q9JZ38 |
| B | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 187 | 44% helix, 25% strand | Q9JZ38 |
| C, j | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 191 | 43% helix, 26% strand | Q9JZ38 |
| D, I, e, i | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 191 | 44% helix, 27% strand | Q9JZ38 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 43% helix, 28% strand | Q9JZ38 |
| F, H, M, a, h | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 191 | 44% helix, 27% strand | Q9JZ38 |
| G, J, L, N, l | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 193 | 44% helix, 26% strand | Q9JZ38 |
| K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 193 | 43% helix, 25% strand | Q9JZ38 |
| b | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 188 | 45% helix, 25% strand | Q9JZ38 |
| c | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 177 | 47% helix, 23% strand | Q9JZ38 |
| d | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 184 | 45% helix, 24% strand | Q9JZ38 |
| f | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 183 | 46% helix, 24% strand | Q9JZ38 |
| g, n | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 192 | 43% helix, 26% strand | Q9JZ38 |
| k | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 194 | 43% helix, 27% strand | Q9JZ38 |
| O, P, Q, R, S, T, U, V, W, X, Y, Z, o, p, q, r, s, t, u, v, w, x, y, z, 0, 1, 2, 3 | Agonist adep A54556 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- OTT · (2E,4E,6E)-octa-2,4,6-trienoic acid · ligand · 28 copies · chains A, G, O, B, P, C, Q, D, R, E, S, F, T, U, H, N, V, I, W, J, X, K, Y, L, Z, M, o, p, a, g, q, b, r, c, s, d, t, e, u, f, v, w, h, n, x, i, y, j, z, k, 0, l, 1, m, 2, 3
- K · Potassium ion · metal · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, a, b, c, d, e, f, g, h, i, j, k, l, m, n
- NA · Sodium ion · metal · 3 copies · chains c, t, h, y, k, 1
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 | 1022 | 0.78 | 0.79 | 119 | empty |
| 2 | 768 | 0.73 | 0.78 | 98 | empty |
| 3 | 427 | 0.71 | 0.81 | 47 | empty |
| 4 | 638 | 0.71 | 0.78 | 73 | empty |
| 5 | 378 | 0.70 | 0.82 | 46 | empty |
Interfaces
128 interfaces between chains.
- j–k · 1736 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 1732 Ų buried · 15 hydrogen bonds · protein-protein
- k–l · 1726 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1678 Ų buried · 11 hydrogen bonds · protein-protein
- M–N · 1622 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified, 28 covalent (nonstandard, covalent ligand).
Compared structures
- 5DKP · Crystal Structure of N. meningitidis ClpP in complex with agonist ADEP A54556. · the same entry in another collection · chain K against K, 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 Q9JZ38
- Elsewhere: RCSB PDB 5DKP · PDBe 5DKP · UniProt Q9JZ38
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