MolNFT v1 · #746 · protein
Antagonist HIV-1 gag peptides induce structural changes in HLA B8-HIV-1 gag peptide (ggkkkykl-index peptide)
1AGD · B*0801: “Antagonist HIV-1 gag peptides induce structural changes in HLA B8-HIV-1 gag peptide (ggkkkykl-index peptide)”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #746 on GenesisL1: 3D structure, binding sites…
- PDB
- 1AGD
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B*0801; Beta-2 microglobulin; HIV-1 gag peptide (ggkkkykl - index peptide)
- UniProt
- P30460, P61769
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B*0801 | protein | 276 | 26% helix, 39% strand | P30460 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | HIV-1 gag peptide (ggkkkykl - index peptide) | protein | 8 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.68 | 0.77 | 54 | empty |
| 2 | 96 | 0.45 | 0.80 | 23 | empty |
| 3 | 141 | 0.43 | 0.76 | 29 | empty |
| 4 | 81 | 0.39 | 0.78 | 15 | empty |
| 5 | 56 | 0.29 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1320 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 817 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1AGD · Antagonist HIV-1 gag peptides induce structural changes in HLA B8-HIV-1 gag peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P30460
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1AGD · PDBe 1AGD · UniProt P30460 · UniProt P61769
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