MolNFT v1 · #137849 · protein
Staphylococcus aureus clpp in complex with (S)-N-((2R,6S,8AS,14AS,20S, 23AS)-2,6-dimethyl-5,8,14,19,23-pentaoxooctadecahydro-1H,5H,14H,19H- PYRIDO[2,1-I]DIPYRROLO[2,1-C:2',1'-L][1]OXA[4,7,10, 13]TETRAAZACYCLOHEXADECIN-20-yl)-3-phenyl-2-(3-phenylureido) propanamide
5W18 · ATP-dependent clp protease proteolytic subunit: “Staphylococcus aureus clpp in complex with (S)-N-((2R,6S,8AS,14AS,20S…”. X-ray diffraction, 1 ligand (9V7), 20 pockets (best druggability 0.71). MolNFT v1 #137849 on GenesisL1: 3D…
- PDB
- 5W18
- Type
- protein
- Length
- 2,592 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease proteolytic subunit; 9V7-phe-ser-pro-ycp-ala-MP8
- EC
- 3.4.21.92
- UniProt
- Q2G036
- Ligands
- 9V7
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 7 distinct chains · 47% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, M, N | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 25% strand | Q2G036 |
| B, D, G, K, L | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 180 | 47% helix, 25% strand | Q2G036 |
| E | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 25% strand | Q2G036 |
| I | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 179 | 47% helix, 24% strand | Q2G036 |
| S | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 24% strand | Q2G036 |
| T | ATP-dependent clp protease proteolytic subunit (EC 3.4.21.92) | protein | 178 | 47% helix, 24% strand | Q2G036 |
| H, J, O, P, Q, R, U, V, X, Y, Z, a, b, c | 9V7-phe-ser-pro-ycp-ala-MP8 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- 9V7 · Phenylcarbamic acid · ligand · 14 copies · chains A, B, H, C, J, D, O, E, P, F, Q, G, R, U, I, K, V, L, X, M, Y, N, Z, S, a, T, b, c
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.71 | 0.79 | 98 | empty |
| 2 | 741 | 0.71 | 0.77 | 101 | empty |
| 3 | 431 | 0.68 | 0.80 | 66 | empty |
| 4 | 446 | 0.66 | 0.79 | 63 | empty |
| 5 | 84 | 0.63 | 0.90 | 18 | empty |
Interfaces
63 interfaces between chains.
- L–M · 1308 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1303 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1292 Ų buried · 13 hydrogen bonds · protein-protein
- M–N · 1278 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1273 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 14 covalent (nonstandard, covalent ligand).
Compared structures
- 5W18 · Staphylococcus aureus ClpP in complex with (S)-N-((2R,6S,8aS,14aS,20S,23aS)-2,6-dimethyl-5… · the same entry in another collection · chain M against M, 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 Q2G036
- Elsewhere: RCSB PDB 5W18 · PDBe 5W18 · UniProt Q2G036
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