MolNFT v1 · #156798 · protein
Crystal structure of the RV305 C1-C2 specific adcc potent antibody DH677.3 Fab in complex with HIV-1 clade A/E GP120 and M48U1
6MFP · Clade A/E 93TH057 HIV-1 GP120 core: “Crystal structure of the RV305 C1-C2 specific adcc potent antibody DH677.3 Fab in complex with HIV-1 clade…”. X-ray diffraction, 5 ligands (MPT, NAG, FUC), 18 pockets (best druggability 0.67).…
- PDB
- 6MFP
- Type
- protein
- Length
- 1,599 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; M48U1 CD4 mimetic peptide; DH677.3 Fab heavy chain…
- UniProt
- A0A0M3KKW9
- Ligands
- MPT, NAG, FUC, NH2, CL
- Pockets
- 18 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A | Clade A/E 93TH057 HIV-1 GP120 core | protein | 341 | 15% helix, 31% strand | A0A0M3KKW9 |
| N, M | M48U1 CD4 mimetic peptide | protein | 26 | 35% helix, 23% strand | — |
| H | DH677.3 Fab heavy chain | protein | 220 | 5% helix, 46% strand | — |
| L, D | DH677.3 Fab light chain | protein | 213 | 7% helix, 48% strand | — |
| C | DH677.3 Fab heavy chain | protein | 219 | 7% helix, 42% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · 2 copies · chains G, N, A, M
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains C, G, H, A
- FUC · alpha-L-fucopyranose · sugar · chains C
- NH2 · Amino group · ion · 2 copies · chains N, M
- CL · Chloride ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.67 | 0.94 | 23 | empty |
| 2 | 603 | 0.65 | 0.75 | 50 | NAG |
| 3 | 645 | 0.64 | 0.75 | 53 | NAG |
| 4 | 666 | 0.64 | 0.74 | 62 | empty |
| 5 | 164 | 0.63 | 0.85 | 30 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1846 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1839 Ų buried · 12 hydrogen bonds · protein-protein
- A–M · 746 Ų buried · 9 hydrogen bonds · protein-protein
- G–N · 737 Ų buried · 10 hydrogen bonds · protein-protein
- G–L · 543 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 24 glycan, 4 covalent, 2 d-amino, 2 modified (disulfide, N-glycosylation, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 6MFP · Crystal Structure of the RV305 C1-C2 specific ADCC potent antibody DH677.3 Fab in complex… · the same entry in another collection · chain G against G, 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 A0A0M3KKW9
- Elsewhere: RCSB PDB 6MFP · PDBe 6MFP · UniProt A0A0M3KKW9
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