MolNFT v1 · #118182 · protein
Crystal structure of HIV-1 integrase catalytic core in complex with Fab
5EU7: “Crystal structure of HIV-1 integrase catalytic core in complex with Fab”. X-ray diffraction, 14 pockets (best druggability 0.64). MolNFT v1 #118182 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EU7
- Type
- protein
- Length
- 1,166 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Fab heavy chain; Fab light chain
- EC
- 2.7.7.-
- UniProt
- P04585
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrase (EC 2.7.7.-) | protein | 143 | 50% helix, 22% strand | P04585 |
| B | Integrase (EC 2.7.7.-) | protein | 144 | 51% helix, 22% strand | P04585 |
| E | Fab heavy chain | protein | 228 | 9% helix, 52% strand | — |
| F | Fab heavy chain | protein | 227 | 8% helix, 53% strand | — |
| D | Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| C | Fab light chain | protein | 211 | 6% helix, 52% strand | — |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.64 | 0.81 | 46 | empty |
| 2 | 337 | 0.61 | 0.78 | 44 | empty |
| 3 | 304 | 0.61 | 0.79 | 46 | empty |
| 4 | 201 | 0.58 | 0.80 | 26 | empty |
| 5 | 210 | 0.58 | 0.80 | 27 | empty |
Interfaces
9 interfaces between chains.
- F–D · 1854 Ų buried · 18 hydrogen bonds · protein-protein
- E–C · 1850 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1563 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 903 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 898 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5EU7 · Crystal structure of HIV-1 integrase catalytic core in complex with Fab · 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 P04585
- Elsewhere: RCSB PDB 5EU7 · PDBe 5EU7 · UniProt P04585
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