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Crystal structure of the RV144 C1-C2 specific antibody CH54 Fab in complex with HIV-1 clade A/E GP120 and M48U1
Analyse Crystal structure of the RV144 C1-C2 specific antibody CH54 Fab in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MG7
- Type
- protein
- Length
- 784 residues
- Chains
- 4
- 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; CH54 Fab heavy chain; CH54…
- UniProt
- A0A0M3KKW9
- Ligands
- MPT, NAG, NH2
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 330 | 15% helix, 35% strand | A0A0M3KKW9 |
| N | M48U1 CD4 mimetic peptide | protein | 26 | 38% helix, 31% strand | — |
| H | CH54 Fab heavy chain | protein | 218 | 7% helix, 47% strand | — |
| L | CH54 Fab light chain | protein | 210 | 4% helix, 43% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · chains G, N
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G, H
- NH2 · Amino group · ion · chains N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.68 | 0.96 | 23 | empty |
| 2 | 205 | 0.62 | 0.82 | 32 | empty |
| 3 | 262 | 0.60 | 0.79 | 36 | empty |
| 4 | 88 | 0.54 | 0.85 | 24 | empty |
| 5 | 79 | 0.52 | 0.85 | 21 | NAG |
Interfaces
4 interfaces between chains.
- H–L · 1764 Ų buried · 11 hydrogen bonds · protein-protein
- G–N · 724 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 639 Ų buried · 2 hydrogen bonds · protein-protein
- G–L · 458 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 10 glycan, 2 covalent, 1 d-amino, 1 modified (disulfide, N-glycosylation, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 6MG7 · Crystal structure of the RV144 C1-C2 specific antibody CH54 Fab in complex with HIV-1… · 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 6MG7 · PDBe 6MG7 · UniProt A0A0M3KKW9
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