MolNFT v1 · #160032 · protein
Crystal structure of antibody P-P3B3 A60C heavy chain in complex with 426C HIV-1 GP120 core G459C
6P8M: “Crystal structure of antibody P-P3B3 A60C heavy chain in complex with 426C HIV-1 GP120 core G459C”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 9 pockets (best druggability 0.67). MolNFT v1 #160032 on GenesisL1: 3D structure…
- PDB
- 6P8M
- Type
- protein
- Length
- 753 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP120; P-P3B3 heavy chain; P-P3B3 light chain
- Ligands
- NAG, MAN, BMA, NA, NH4, CL
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | GP120 | protein | 333 | 17% helix, 38% strand | — |
| H | P-P3B3 heavy chain | protein | 216 | 8% helix, 49% strand | — |
| L | P-P3B3 light chain | protein | 204 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains C, H
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains C
- BMA · beta-D-mannopyranose · sugar
- NA · Sodium ion · metal · 4 copies · chains C, H
- NH4 · Ammonium ion · ion · 4 copies · chains C
- CL · Chloride ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.67 | 0.80 | 48 | empty |
| 2 | 53 | 0.60 | 0.92 | 22 | empty |
| 3 | 98 | 0.58 | 0.86 | 22 | NAG |
| 4 | 458 | 0.57 | 0.73 | 58 | empty |
| 5 | 309 | 0.52 | 0.74 | 34 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1532 Ų buried · 14 hydrogen bonds · protein-protein
- C–H · 906 Ų buried · 23 hydrogen bonds · protein-protein
- C–L · 229 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6P8M · Crystal Structure of Antibody P-p3b3 A60C Heavy Chain in Complex with 426c HIV-1 gp120… · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 6P8M · PDBe 6P8M
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.