Research workbench
BG505 SOSIP.664 with 2G12 FAB2
Analyse BG505 SOSIP.664 with 2G12 FAB2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OZC
- Type
- protein
- Length
- 3,027 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Envelope glycoprotein GP41; 2G12 Fab light chain; 2G12 Fab…
- UniProt
- Q2N0S6
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Envelope glycoprotein GP160 | protein | 435 | 14% helix, 39% strand | Q2N0S6 |
| B, G, I | Envelope glycoprotein GP41 | protein | 120 | 59% helix, 4% strand | Q2N0S6 |
| L, D, Q, M, R, N | 2G12 Fab light chain | protein | 105 | 3% helix, 50% strand | — |
| H, C, O, J, P, K | 2G12 Fab heavy chain | protein | 122 | 10% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 84 copies · chains A, L, H, C, D, E, Q, O, J, M, F, R, P, K, N
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 81 copies · chains A, E, F, B, G, I
- BMA · beta-D-mannopyranose · sugar · 21 copies · chains H, O, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.80 | 0.93 | 26 | empty |
| 2 | 1002 | 0.76 | 0.78 | 111 | empty |
| 3 | 957 | 0.71 | 0.75 | 93 | empty |
| 4 | 80 | 0.68 | 0.93 | 27 | empty |
| 5 | 519 | 0.68 | 0.78 | 59 | empty |
Interfaces
24 interfaces between chains.
- E–G · 2313 Ų buried · 21 hydrogen bonds · protein-protein
- F–I · 2310 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2304 Ų buried · 21 hydrogen bonds · protein-protein
- G–I · 994 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 992 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6OZC · BG505 SOSIP.664 with 2G12 Fab2 · 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
- Elsewhere: RCSB PDB 6OZC · PDBe 6OZC · UniProt Q2N0S6
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