MolNFT v2 · #116962 · protein
Crystal Structure of N. meningitidis ClpP in complex with agonist ADEP A54556.
5DKP: “Crystal Structure of N. meningitidis ClpP in complex with agonist ADEP A54556.”. X-ray diffraction at 2.381, 2 ligands (K, NA). MolNFT v2 #116962 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DKP
- Type
- protein
- Length
- 5,496 residues
- Chains
- 56
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.381
- Source
- Neisseria meningitidis serogroup B (strain MC58); SYNTHETIC CONSTRUCT
- UniProt
- Q9JZ38
- Ligands
- K, NA
Structure
x-ray diffraction · resolution 2.381 · 15 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, m | — | protein | 190 | — | Q9JZ38 |
| B | — | protein | 187 | — | Q9JZ38 |
| C, j | — | protein | 191 | — | Q9JZ38 |
| D, I, e, i | — | protein | 191 | — | Q9JZ38 |
| E | — | protein | 192 | — | Q9JZ38 |
| F, H, M, a, h | — | protein | 191 | — | Q9JZ38 |
| G, J, L, N, l | — | protein | 193 | — | Q9JZ38 |
| K | — | protein | 193 | — | Q9JZ38 |
| b | — | protein | 188 | — | Q9JZ38 |
| c | — | protein | 177 | — | Q9JZ38 |
| d | — | protein | 184 | — | Q9JZ38 |
| f | — | protein | 183 | — | Q9JZ38 |
| g, n | — | protein | 192 | — | Q9JZ38 |
| k | — | protein | 194 | — | 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 | — | protein | 6 | — | — |
Ligands and binding sites
- 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, h, k, 1
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5DKP · Crystal structure of N. meningitidis clpp in complex with agonist adep A54556. · the same entry in another collection · chain G against G, 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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