MolNFT v1 · #180003 · protein
Crystal structure of a HIV-1 clade C isolate DU172.17 HR1.R4.664 env trimer in complex with human fabs PGT124 and 35O22
7KMD · 35O22 heavy chain: “Crystal structure of a HIV-1 clade C isolate DU172.17 HR1.R4.664 env trimer in complex with human fabs PGT124…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 7KMD
- Type
- protein
- Length
- 1,469 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 35O22 heavy chain; 35O22 light chain; Envelope glycoprotein GP120; Envelope glycoprotein…
- UniProt
- Q202J8
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 35O22 heavy chain | protein | 240 | 2% helix, 48% strand | — |
| E | 35O22 light chain | protein | 213 | 6% helix, 46% strand | — |
| G | Envelope glycoprotein GP120 | protein | 447 | 12% helix, 34% strand | Q202J8 |
| T | Envelope glycoprotein GP41 | protein | 134 | 48% helix, 5% strand | — |
| L | 124 light chain | protein | 210 | 5% helix, 43% strand | — |
| H | 124 heavy chain | protein | 225 | 5% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, G, T, L, H, E
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, E, G, L, H
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, E, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.78 | 0.86 | 69 | NAG |
| 2 | 88 | 0.65 | 0.91 | 17 | empty |
| 3 | 116 | 0.64 | 0.88 | 20 | empty |
| 4 | 331 | 0.61 | 0.78 | 41 | empty |
| 5 | 459 | 0.57 | 0.73 | 63 | empty |
Interfaces
8 interfaces between chains.
- G–T · 2712 Ų buried · 23 hydrogen bonds · protein-protein
- L–H · 1996 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1800 Ų buried · 14 hydrogen bonds · protein-protein
- A–T · 404 Ų buried · 5 hydrogen bonds · protein-protein
- G–L · 340 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 21 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7KMD · Crystal structure of a HIV-1 clade C isolate Du172.17 HR1.R4.664 Env trimer in complex… · 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 Q202J8
- Elsewhere: RCSB PDB 7KMD · PDBe 7KMD · UniProt Q202J8
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