MolNFT v1 · #146275 · protein
Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab
6DCQ · Envelope glycoprotein GP160: “Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab”. Electron microscopy, 5 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6DCQ
- Type
- protein
- Length
- 2,231 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Immunoglobulin G PGT151 Fab, heavy chain; Immunoglobulin G…
- UniProt
- A0A2H4K974, S6B291, Q8TCD0
- Ligands
- NAG, MAN, BMA, FUC, GAL
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 10 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP160 | protein | 435 | 11% helix, 35% strand | A0A2H4K974 |
| B | Envelope glycoprotein GP160 | protein | 122 | 44% helix, 7% strand | A0A2H4K974 |
| C | Envelope glycoprotein GP160 | protein | 452 | 10% helix, 38% strand | A0A2H4K974 |
| D | Envelope glycoprotein GP160 | protein | 146 | 47% helix, 5% strand | A0A2H4K974 |
| E | Envelope glycoprotein GP160 | protein | 448 | 11% helix, 37% strand | A0A2H4K974 |
| F | Envelope glycoprotein GP160 | protein | 139 | 43% helix, 9% strand | A0A2H4K974 |
| H | Immunoglobulin G PGT151 Fab, heavy chain | protein | 132 | 2% helix, 19% strand | S6B291 |
| L | Immunoglobulin G PGT151 Fab, light chain | protein | 110 | 0% helix, 33% strand | Q8TCD0 |
| M | Immunoglobulin G PGT151 Fab, heavy chain | protein | 135 | 0% helix, 48% strand | S6B291 |
| N | Immunoglobulin G PGT151 Fab, light chain | protein | 112 | 0% helix, 45% strand | Q8TCD0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 100 copies · chains A, C, B, E, D, M, F, N, H, L
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, C, M, N, E, H, L
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains M, H
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, C, D, M, E, F, H
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains F, M, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.81 | 0.82 | 87 | empty |
| 2 | 887 | 0.79 | 0.82 | 85 | empty |
| 3 | 1034 | 0.78 | 0.80 | 111 | empty |
| 4 | 560 | 0.77 | 0.83 | 69 | NAG |
| 5 | 290 | 0.74 | 0.87 | 50 | NAG |
Interfaces
24 interfaces between chains.
- C–D · 3169 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2898 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2266 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1148 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 1134 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 59 glycan, 34 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6DCQ · Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with… · 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 A0A2H4K974
- Every structure of UniProt S6B291
- Every structure of UniProt Q8TCD0
- Elsewhere: RCSB PDB 6DCQ · PDBe 6DCQ · UniProt A0A2H4K974 · UniProt S6B291 · UniProt Q8TCD0
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