Research workbench
Crystal structure analysis of HIV-1 subtype C protease complexed with indinavir
Analyse Crystal structure analysis of HIV-1 subtype C protease complexed with indinavir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R5P
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- UniProt
- Q50CM2
- Ligands
- MK1, NA, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease | protein | 99 | 7% helix, 54% strand | Q50CM2 |
Ligands and binding sites
- MK1 · N-[2(R)-hydroxy-1(S)-indanyl]-5-[(2(S)-tertiary butylaminocarbonyl)-4(3-pyridylmethyl)piperazino]-4(S)-hydroxy-2(R)-phenylmethylpentanamide · ligand · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.73 | 0.85 | 34 | MK1 |
| 2 | 358 | 0.73 | 0.85 | 37 | MK1 |
| 3 | 159 | 0.45 | 0.75 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1890 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1881 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 227 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2R5P · Crystal Structure Analysis of HIV-1 Subtype C Protease Complexed with Indinavir · the same entry in another collection · chain A against A, 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 Q50CM2
- Elsewhere: RCSB PDB 2R5P · PDBe 2R5P · UniProt Q50CM2
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