Research workbench
Hsluv (H. influenzae)-nlvs vinyl sulfone inhibitor complex
Analyse Hsluv (H. influenzae)-nlvs vinyl sulfone inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KYI
- Type
- protein
- Length
- 5,904 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent hsl protease ATP-binding subunit hslu; ATP-dependent protease hslv
- EC
- 3.4.99.-
- UniProt
- P43773, P43772
- Ligands
- ATP, LVS
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | ATP-dependent hsl protease ATP-binding subunit hslu | protein | 321 | 55% helix, 13% strand | P43773 |
| G, H, I, J, K, L, M, N, O, P, Q, R | ATP-dependent protease hslv (EC 3.4.99.-) | protein | 173 | 31% helix, 30% strand | P43772 |
| S, T, U, V, W, X | ATP-dependent hsl protease ATP-binding subunit hslu | protein | 317 | 37% helix, 13% strand | P43773 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains A, B, C, D, E, F, S, X, T, U, V, W
- LVS · 4-iodo-3-nitrophenyl acetyl-leucinyl-leucinyl-leucinyl-vinylsulfone · ligand · 12 copies · chains F, G, L, A, H, B, I, C, J, D, K, E, M, N, O, P, Q, R
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 | 1102 | 0.85 | 0.86 | 112 | ATP |
| 2 | 997 | 0.85 | 0.86 | 89 | ATP |
| 3 | 1075 | 0.85 | 0.86 | 106 | ATP |
| 4 | 1067 | 0.85 | 0.86 | 116 | ATP |
| 5 | 1020 | 0.84 | 0.85 | 84 | ATP |
Interfaces
72 interfaces between chains.
- U–V · 1646 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1632 Ų buried · 23 hydrogen bonds · protein-protein
- V–W · 1629 Ų buried · 15 hydrogen bonds · protein-protein
- S–T · 1620 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1608 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 1KYI · HslUV (H. influenzae)-NLVS Vinyl Sulfone Inhibitor Complex · 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 P43773
- Every structure of UniProt P43772
- Elsewhere: RCSB PDB 1KYI · PDBe 1KYI · UniProt P43773 · UniProt P43772
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