Research workbench
Asymmetric model of CD4- and 17-bound B41 HIV-1 env sosip in complex with ddm
Analyse Asymmetric model of CD4- and 17-bound B41 HIV-1 env sosip in complex with ddm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OPP
- Type
- protein
- Length
- 2,565 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 17B Fab light chain; Envelope glycoprotein GP41; Envelope glycoprotein GP160; T-cell…
- UniProt
- B3UEZ6, B3UES2, P01730
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 8 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, I, O | 17B Fab light chain | protein | 110 | 3% helix, 47% strand | — |
| B | Envelope glycoprotein GP41 | protein | 135 | 64% helix, 7% strand | B3UEZ6 |
| A, D | Envelope glycoprotein GP160 | protein | 389 | 14% helix, 38% strand | B3UES2 |
| C, M, F | T-cell surface glycoprotein CD4 | protein | 97 | 9% helix, 45% strand | P01730 |
| H, G, N | 17B Fab heavy chain | protein | 127 | 7% helix, 46% strand | — |
| E | Envelope glycoprotein GP41 | protein | 138 | 62% helix, 7% strand | B3UEZ6 |
| K | Envelope glycoprotein GP41 | protein | 130 | 64% helix, 7% strand | B3UEZ6 |
| J | Envelope glycoprotein GP160 | protein | 382 | 15% helix, 37% strand | B3UES2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 90 copies · chains A, D, J, M, B, E, K
- BMA · beta-D-mannopyranose · sugar · 17 copies · chains D, J
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, D, F, J, M
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains B, K, E
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 | 679 | 0.75 | 0.81 | 52 | LMT |
| 2 | 566 | 0.73 | 0.80 | 52 | LMT |
| 3 | 521 | 0.73 | 0.81 | 47 | empty |
| 4 | 65 | 0.72 | 0.97 | 20 | empty |
| 5 | 67 | 0.72 | 0.98 | 27 | empty |
Interfaces
24 interfaces between chains.
- D–E · 2305 Ų buried · 27 hydrogen bonds · protein-protein
- B–A · 2290 Ų buried · 27 hydrogen bonds · protein-protein
- K–J · 2188 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1207 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1179 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6OPP · Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM · the same entry in another collection · chain F against F, 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 B3UEZ6
- Every structure of UniProt B3UES2
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 6OPP · PDBe 6OPP · UniProt B3UEZ6 · UniProt B3UES2 · UniProt P01730
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