MolNFT v1 · #159515 · protein
Modified BG505 sosip-based immunogen RC1 in complex with the elicited V3-glycan patch antibody AB897NHP
6ORP · RC1 variant of HIV-1 env glycoprotein GP41: “Modified BG505 sosip-based immunogen RC1 in complex with the elicited V3-glycan patch antibody AB897NHP”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability…
- PDB
- 6ORP
- Type
- protein
- Length
- 2,397 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RC1 variant of HIV-1 env glycoprotein GP41; RC1 variant of HIV-1 env glycoprotein GP120…
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 14% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | RC1 variant of HIV-1 env glycoprotein GP41 | protein | 124 | 48% helix, 2% strand | — |
| B, G, I | RC1 variant of HIV-1 env glycoprotein GP120 | protein | 442 | 10% helix, 34% strand | — |
| D, H, J | AB897NHP antibody Fab heavy chain | protein | 124 | 2% helix, 26% strand | — |
| E, K, L | AB897NHP antibody Fab light chain | protein | 109 | 4% helix, 17% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 80 copies · chains B, G, C, H, I, J, A, F
- BMA · beta-D-mannopyranose · sugar · 13 copies
- MAN · alpha-D-mannopyranose · sugar · 5 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.83 | 0.90 | 47 | empty |
| 2 | 476 | 0.82 | 0.89 | 79 | empty |
| 3 | 379 | 0.81 | 0.89 | 60 | NAG |
| 4 | 1004 | 0.80 | 0.81 | 121 | empty |
| 5 | 237 | 0.79 | 0.92 | 65 | empty |
Interfaces
21 interfaces between chains.
- C–G · 2206 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 2183 Ų buried · 2 hydrogen bonds · protein-protein
- F–I · 2163 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 812 Ų buried · 7 hydrogen bonds · protein-protein
- H–L · 806 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 30 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ORP · Modified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch… · the same entry in another collection · chain J against J, 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 6ORP · PDBe 6ORP
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