MolNFT v1 · #158219 · protein
Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to VRC01 FR3-03 scfv in complex with crystallization chaperones 3H109L Fab and 35O22 scfv at 3.5 ångström
6NNF · Envelope glycoprotein GP41: “Crystal structure of HIV-1 BG505 SOSIP.664 prefusion env trimer bound to VRC01 FR3-03 scfv in complex with…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 6NNF
- Type
- protein
- Length
- 1,462 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP41; 35O22 scfv heavy chain; 35O22 scfv light chain; Envelope…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP41 | protein | 130 | 52% helix, 5% strand | Q2N0S6 |
| D | 35O22 scfv heavy chain | protein | 128 | 5% helix, 37% strand | — |
| E | 35O22 scfv light chain | protein | 112 | 3% helix, 43% strand | — |
| G | Envelope glycoprotein GP120 | protein | 431 | 12% helix, 40% strand | Q2N0S6 |
| H | 3H109L Fab heavy chain | protein | 227 | 7% helix, 48% strand | — |
| L | 3H109L Fab light chain | protein | 211 | 5% helix, 44% strand | — |
| U | VRC01 FR3-03 heavy chain | protein | 126 | 5% helix, 44% strand | — |
| V | VRC01 FR3-03 light chain | protein | 97 | 0% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains B, D, G, L, U, V, H
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains D, E, G, H, L
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, E, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.70 | 0.85 | 49 | NAG |
| 2 | 443 | 0.67 | 0.79 | 48 | empty |
| 3 | 258 | 0.65 | 0.83 | 29 | empty |
| 4 | 265 | 0.63 | 0.81 | 43 | empty |
| 5 | 223 | 0.61 | 0.81 | 27 | empty |
Interfaces
11 interfaces between chains.
- B–G · 2646 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1941 Ų buried · 13 hydrogen bonds · protein-protein
- G–U · 1013 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 992 Ų buried · 10 hydrogen bonds · protein-protein
- U–V · 770 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 6NNF · Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to VRC01 FR3-03… · the same entry in another collection · chain B against B, 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 6NNF · PDBe 6NNF · UniProt Q2N0S6
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