MolNFT v1 · #157075 · protein
Rhesus macaque anti-HIV V3 antibody DH727.2 with GP120 V3 ZAM18 peptide
6MNQ · Envelope glycoprotein: “Rhesus macaque anti-HIV V3 antibody DH727.2 with GP120 V3 ZAM18 peptide”. X-ray diffraction, 4 pockets (best druggability 0.57). MolNFT v1 #157075 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MNQ
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein; Ab DH727.2 heavy chain Fab fragment; Ab DH727.2 light chain
- UniProt
- A0A0K0KAD3
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Envelope glycoprotein | protein | 12 | 0% helix, 58% strand | A0A0K0KAD3 |
| H | Ab DH727.2 heavy chain Fab fragment | protein | 210 | 9% helix, 53% strand | — |
| L | Ab DH727.2 light chain | protein | 219 | 6% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains P, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.57 | 0.75 | 44 | empty |
| 2 | 145 | 0.45 | 0.76 | 27 | empty |
| 3 | 64 | 0.44 | 0.82 | 16 | empty |
| 4 | 82 | 0.33 | 0.74 | 26 | EDO |
Interfaces
3 interfaces between chains.
- H–L · 1737 Ų buried · 15 hydrogen bonds · protein-protein
- P–H · 345 Ų buried · 2 hydrogen bonds · protein-protein
- P–L · 218 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6MNQ · Rhesus macaque anti-HIV V3 antibody DH727.2 with gp120 V3 ZAM18 peptide · the same entry in another collection · chain P against P, 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 A0A0K0KAD3
- Elsewhere: RCSB PDB 6MNQ · PDBe 6MNQ · UniProt A0A0K0KAD3
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