MolNFT v1 · #167470 · protein
BG505 SOSIP.V5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab
6VLR · Envelope glycoprotein GP120: “BG505 SOSIP.V5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.81). MolNFT v1 #167470 on GenesisL1: 3D…
- PDB
- 6VLR
- Type
- protein
- Length
- 2,611 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; BG505 SOSIPV5.2 GP41; PGT122 Fab heavy chain; PGT122 Fab…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 20% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, G | Envelope glycoprotein GP120 | protein | 430 | 13% helix, 44% strand | Q2N0S6 |
| B | BG505 SOSIPV5.2 GP41 | protein | 128 | 56% helix, 4% strand | Q2N0S6 |
| J, I | BG505 SOSIPV5.2 GP41 | protein | 122 | 62% helix, 4% strand | Q2N0S6 |
| C, D, E | PGT122 Fab heavy chain | protein | 132 | 7% helix, 55% strand | — |
| L, K, M | PGT122 Fab light chain | protein | 106 | 3% helix, 43% strand | — |
| F | RM20E1 Fab heavy chain | protein | 123 | 5% helix, 51% strand | — |
| N | RM20E1 Fab kappa chain | protein | 112 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 62 copies · chains A, C, L, B, H, D, K, J, G, E, M, I
- MAN · alpha-D-mannopyranose · sugar · 19 copies · chains C, L, H, D, K, G, E, M
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains C, D, 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 | 463 | 0.81 | 0.88 | 67 | empty |
| 2 | 79 | 0.75 | 0.97 | 26 | empty |
| 3 | 342 | 0.74 | 0.85 | 61 | NAG |
| 4 | 851 | 0.74 | 0.78 | 93 | empty |
| 5 | 64 | 0.72 | 0.98 | 26 | empty |
Interfaces
26 interfaces between chains.
- H–J · 2388 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2251 Ų buried · 25 hydrogen bonds · protein-protein
- G–I · 2198 Ų buried · 23 hydrogen bonds · protein-protein
- C–L · 1168 Ų buried · 17 hydrogen bonds · protein-protein
- D–K · 1117 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 6VLR · BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab · 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
- Every structure of UniProt Q2N0S6
- Elsewhere: RCSB PDB 6VLR · PDBe 6VLR · UniProt Q2N0S6
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