Research workbench
Cryo-EM structure of DH851.3 bound to HIV-1 CH505 env
Analyse Cryo-EM structure of DH851.3 bound to HIV-1 CH505 env in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LU9
- Type
- protein
- Length
- 4,383 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH851.3 light chain; DH851.3 heavy chain; Envelope glycoprotein GP41; Envelope…
- UniProt
- M4M097
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 12% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| k, j, r | DH851.3 light chain | protein | 209 | 5% helix, 30% strand | — |
| l, i, q | DH851.3 heavy chain | protein | 228 | 6% helix, 44% strand | — |
| m, h, p | DH851.3 heavy chain | protein | 222 | 5% helix, 36% strand | — |
| n, g, o | DH851.3 light chain | protein | 206 | 8% helix, 27% strand | — |
| a, b, c | Envelope glycoprotein GP41 | protein | 135 | 55% helix, 7% strand | — |
| d, e, f | Envelope glycoprotein GP120 | protein | 461 | 12% helix, 27% strand | M4M097 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains a, d, h, b, e, l, c, f, q
- BMA · beta-D-mannopyranose · sugar · 18 copies · chains i, d, e, p
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains i, h, g, d, m, l, e, p, q, r, f
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 | 1054 | 0.86 | 0.87 | 135 | empty |
| 2 | 236 | 0.84 | 0.95 | 37 | empty |
| 3 | 900 | 0.83 | 0.85 | 108 | empty |
| 4 | 527 | 0.82 | 0.88 | 76 | empty |
| 5 | 629 | 0.81 | 0.86 | 65 | empty |
Interfaces
26 interfaces between chains.
- a–d · 2502 Ų buried · 26 hydrogen bonds · protein-protein
- c–f · 2482 Ų buried · 25 hydrogen bonds · protein-protein
- b–e · 2431 Ų buried · 24 hydrogen bonds · protein-protein
- m–n · 2251 Ų buried · 35 hydrogen bonds · protein-protein
- i–j · 2209 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 7LU9 · Cryo-EM structure of DH851.3 bound to HIV-1 CH505 Env · the same entry in another collection · chain k against k, 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 M4M097
- Elsewhere: RCSB PDB 7LU9 · PDBe 7LU9 · UniProt M4M097
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