MolNFT v1 · #157076 · protein
Rhesus macaque anti-HIV V3 antibody DH753 with GP120 V3 ZAM18 peptide
6MNR · Envelope glycoprotein: “Rhesus macaque anti-HIV V3 antibody DH753 with GP120 V3 ZAM18 peptide”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.57). MolNFT v1 #157076 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6MNR
- Type
- protein
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein; Ab DH753 heavy chain Fab fragment; Ab DH753 light chain
- UniProt
- A0A0K0KAD3
- Ligands
- SO4
- Pockets
- 3 · 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 | 14 | 0% helix, 50% strand | A0A0K0KAD3 |
| H | Ab DH753 heavy chain Fab fragment | protein | 219 | 8% helix, 54% strand | — |
| L | Ab DH753 light chain | protein | 211 | 6% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.57 | 0.74 | 58 | empty |
| 2 | 124 | 0.39 | 0.74 | 25 | empty |
| 3 | 68 | 0.34 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1615 Ų buried · 18 hydrogen bonds · protein-protein
- P–H · 456 Ų buried · 4 hydrogen bonds · protein-protein
- P–L · 369 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6MNR · Rhesus macaque anti-HIV V3 antibody DH753 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 6MNR · PDBe 6MNR · UniProt A0A0K0KAD3
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