MolNFT v1 · #157787 · protein
Crystal structure of neisseria meningitidis clpp protease in complex with acyldepsipeptide-14 (adep-14)
6NAH · ATP-dependent clp protease proteolytic subunit: “Crystal structure of neisseria meningitidis clpp protease in complex with acyldepsipeptide-14 (adep-14)”. X-ray diffraction, 1 ligand (OCA), 20 pockets (best druggability 0.75).…
- PDB
- 6NAH
- Type
- protein
- Length
- 5,007 residues
- Chains
- 56
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; Acyldepsipeptide-14
- EC
- 3.4.21.92
- UniProt
- I4E574
- Ligands
- OCA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 16 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 175 | 48% helix, 21% strand | I4E574 |
| B, N, P, W | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 49% helix, 21% strand | I4E574 |
| C | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 49% helix, 21% strand | I4E574 |
| D, S, a | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 49% helix, 21% strand | I4E574 |
| E, H, K | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 48% helix, 21% strand | I4E574 |
| F, I, M | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 171 | 49% helix, 22% strand | I4E574 |
| G, Q | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 173 | 48% helix, 21% strand | I4E574 |
| J, O, Y | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 49% helix, 23% strand | I4E574 |
| L, X | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 48% helix, 22% strand | I4E574 |
| R | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 175 | 48% helix, 23% strand | I4E574 |
| T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 171 | 49% helix, 23% strand | I4E574 |
| U | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 174 | 48% helix, 24% strand | I4E574 |
| V | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 171 | 49% helix, 22% strand | I4E574 |
| Z | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 49% helix, 22% strand | I4E574 |
| b | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 172 | 48% helix, 22% strand | I4E574 |
| c, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, 0, 1, 2, 3, 4 | Acyldepsipeptide-14 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- OCA · Octanoic acid (caprylic acid) · ligand · 28 copies · chains A, G, c, B, e, C, f, D, g, E, h, F, i, j, H, N, k, I, l, J, m, K, n, L, o, M, p, q, O, U, r, P, s, Q, t, R, u, S, v, T, w, x, V, b, y, W, z, X, 0, Y, 1, Z, 2, a, 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 | 1120 | 0.75 | 0.78 | 102 | OCA |
| 2 | 790 | 0.72 | 0.77 | 60 | OCA |
| 3 | 634 | 0.72 | 0.79 | 106 | empty |
| 4 | 644 | 0.71 | 0.78 | 95 | empty |
| 5 | 338 | 0.66 | 0.80 | 47 | empty |
Interfaces
114 interfaces between chains.
- Z–a · 1230 Ų buried · 16 hydrogen bonds · protein-protein
- H–N · 1229 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1202 Ų buried · 11 hydrogen bonds · protein-protein
- X–Y · 1201 Ų buried · 11 hydrogen bonds · protein-protein
- R–S · 1200 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 112 modified, 28 covalent (nonstandard, covalent ligand).
Compared structures
- 6NAH · Crystal structure of Neisseria meningitidis ClpP protease in complex with… · the same entry in another collection · chain B against B, 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 I4E574
- Elsewhere: RCSB PDB 6NAH · PDBe 6NAH · UniProt I4E574
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