MolNFT v1 · #118586 · protein
Crystal structure of tier 2 neutralizing antibody DH427 from a rhesus macaque in complex with HIV-1 GP120 core
5F6J · Envelope glycoprotein GP120 of HIV-1 clade C: “Crystal structure of tier 2 neutralizing antibody DH427 from a rhesus macaque in complex with HIV-1 GP120 core”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5F6J
- Type
- protein
- Length
- 1,516 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120 of HIV-1 clade C; DH427 antibody light chain; DH427 antibody…
- UniProt
- R4GRV3
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, E | Envelope glycoprotein GP120 of HIV-1 clade C | protein | 336 | 18% helix, 32% strand | R4GRV3 |
| A, F | DH427 antibody light chain | protein | 212 | 5% helix, 50% strand | — |
| B, H | DH427 antibody heavy chain | protein | 210 | 4% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.80 | 0.97 | 30 | empty |
| 2 | 196 | 0.78 | 0.92 | 40 | empty |
| 3 | 204 | 0.77 | 0.92 | 42 | empty |
| 4 | 251 | 0.75 | 0.89 | 53 | empty |
| 5 | 243 | 0.75 | 0.89 | 53 | empty |
Interfaces
8 interfaces between chains.
- F–H · 1665 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1631 Ų buried · 8 hydrogen bonds · protein-protein
- G–B · 424 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 415 Ų buried · 11 hydrogen bonds · protein-protein
- G–A · 314 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide (disulfide).
Compared structures
- 5F6J · Crystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rhesus Macaque in 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 R4GRV3
- Elsewhere: RCSB PDB 5F6J · PDBe 5F6J · UniProt R4GRV3
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