Research workbench
Cryo-EM structure of CAP256-VRC26.25 Fab bound to HIV-1 env trimer CAP256.WK34.C80 SOSIP.RNS2
Analyse Cryo-EM structure of CAP256-VRC26.25 Fab bound to HIV-1 env trimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VTT
- Type
- protein
- Length
- 1,928 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; VRC26.25 heavy chain; VRC26.25 light chain; Envelope…
- UniProt
- A2NUT2
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 8 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Envelope glycoprotein GP120 | protein | 430 | 9% helix, 37% strand | — |
| E | Envelope glycoprotein GP120 | protein | 431 | 9% helix, 35% strand | — |
| G | Envelope glycoprotein GP120 | protein | 436 | 10% helix, 31% strand | — |
| H | VRC26.25 heavy chain | protein | 143 | 6% helix, 48% strand | — |
| L | VRC26.25 light chain | protein | 108 | 3% helix, 39% strand | A2NUT2 |
| A | Envelope glycoprotein GP41 | protein | 124 | 65% helix, 3% strand | — |
| B | Envelope glycoprotein GP41 | protein | 129 | 53% helix, 5% strand | — |
| C | Envelope glycoprotein GP41 | protein | 127 | 54% helix, 6% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 85 copies · chains F, H, G, E, A, C, B
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains F, E, H, L, G
- BMA · beta-D-mannopyranose · sugar · 7 copies
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 | 810 | 0.88 | 0.90 | 101 | empty |
| 2 | 282 | 0.78 | 0.89 | 46 | empty |
| 3 | 710 | 0.73 | 0.79 | 84 | empty |
| 4 | 270 | 0.72 | 0.85 | 40 | NAG |
| 5 | 205 | 0.71 | 0.88 | 40 | NAG |
Interfaces
17 interfaces between chains.
- E–C · 2794 Ų buried · 17 hydrogen bonds · protein-protein
- G–B · 2757 Ų buried · 12 hydrogen bonds · protein-protein
- F–A · 2654 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1108 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 1072 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 33 disulfide, 2 modified (N-glycosylation, disulfide, sulfation).
Compared structures
- 6VTT · Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80… · the same entry in another collection · chain C against C, TM-score 1.00
- 5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain L against L, TM-score 0.89
- 5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain L against L, TM-score 0.89
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 A2NUT2
- Elsewhere: RCSB PDB 6VTT · PDBe 6VTT · UniProt A2NUT2
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