Research workbench
VRC03 and 10-1074 bound BG505 F14 HIV-1 sosip envelope trimer structure
Analyse VRC03 and 10-1074 bound BG505 F14 HIV-1 sosip envelope trimer structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V8Z
- Type
- protein
- Length
- 4,416 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; 10-1074 Fab heavy chain; 10-1074…
- UniProt
- Q2N0S6, Q2N0S7, Q6N089, Q8N5F4, P0DOX5, Q6P5S8
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, M | Envelope glycoprotein GP120 | protein | 449 | 10% helix, 36% strand | Q2N0S6 |
| B, H, N | Envelope glycoprotein GP41 | protein | 147 | 51% helix, 5% strand | Q2N0S7 |
| D, J, P | 10-1074 Fab heavy chain | protein | 230 | 4% helix, 47% strand | Q6N089 |
| E, K, Q | 10-1074 Fab light chain | protein | 211 | 3% helix, 40% strand | Q8N5F4 |
| C, I, O | VRC03 Fab heavy chain | protein | 227 | 4% helix, 52% strand | P0DOX5 |
| F, L, R | VRC03 Fab light chain | protein | 208 | 4% helix, 39% strand | Q6P5S8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, B, D, E, G, H, J, K, M, N, P, Q, C, F, I, L, O, R
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains D, E, A, J, K, G, P, Q, M
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains D, J, P
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 | 1186 | 0.84 | 0.85 | 130 | empty |
| 2 | 1160 | 0.82 | 0.83 | 119 | empty |
| 3 | 452 | 0.80 | 0.88 | 65 | empty |
| 4 | 1003 | 0.79 | 0.81 | 90 | empty |
| 5 | 443 | 0.78 | 0.86 | 60 | empty |
Interfaces
36 interfaces between chains.
- A–B · 3198 Ų buried · 21 hydrogen bonds · protein-protein
- M–N · 3194 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 3188 Ų buried · 21 hydrogen bonds · protein-protein
- P–Q · 2169 Ų buried · 10 hydrogen bonds · protein-protein
- J–K · 2164 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 disulfide, 57 glycan (disulfide, N-glycosylation).
Compared structures
- 6V8Z · VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure · 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 Q2N0S6
- Every structure of UniProt Q2N0S7
- Every structure of UniProt Q6N089
- Every structure of UniProt Q8N5F4
- Every structure of UniProt P0DOX5
- Every structure of UniProt Q6P5S8
- Elsewhere: RCSB PDB 6V8Z · PDBe 6V8Z · UniProt Q2N0S6 · UniProt Q2N0S7 · UniProt Q6N089 · UniProt Q8N5F4 · UniProt P0DOX5 · UniProt Q6P5S8
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