MolNFT v1 · #143958 · protein
Crystal structure of HIV-1 clade ae strain CNE55 GP120 core in complex with neutralizing antibody vrc-PG05 that targets the center of the silent face on the outer domain of GP120
6BF4 · HIV-1 clade ae GP120 core: “Crystal structure of HIV-1 clade ae strain CNE55 GP120 core in complex with neutralizing antibody vrc-PG05…”. X-ray diffraction, 2 ligands (MAN, NAG), 19 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 6BF4
- Type
- protein
- Length
- 1,553 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 clade ae GP120 core; Vrc-PG05 Fab heavy chain; Vrc-PG05 Fab light chain
- Ligands
- MAN, NAG
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 clade ae GP120 core | protein | 337 | 15% helix, 36% strand | — |
| B | Vrc-PG05 Fab heavy chain | protein | 225 | 4% helix, 54% strand | — |
| C | Vrc-PG05 Fab light chain | protein | 219 | 6% helix, 53% strand | — |
| G | HIV-1 clade ae GP120 core | protein | 333 | 18% helix, 38% strand | — |
| H | Vrc-PG05 Fab heavy chain | protein | 221 | 5% helix, 56% strand | — |
| L | Vrc-PG05 Fab light chain | protein | 218 | 7% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 41 copies · chains B, A, C, G, H, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C, G, H, L
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, B, G, L, H
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.76 | 0.80 | 82 | NAG |
| 2 | 691 | 0.67 | 0.76 | 60 | EDO |
| 3 | 698 | 0.65 | 0.74 | 55 | EDO |
| 4 | 60 | 0.58 | 0.90 | 22 | empty |
| 5 | 56 | 0.56 | 0.89 | 21 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2085 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1893 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 757 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 282 Ų buried · 2 hydrogen bonds · protein-protein
- G–L · 178 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 22 glycan (disulfide, N-glycosylation).
Compared structures
- 6BF4 · Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing… · 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
- Elsewhere: RCSB PDB 6BF4 · PDBe 6BF4
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