Research workbench
Crystal structure of HIV-1 broadly neutralizing antibody ACS202
Analyse Crystal structure of HIV-1 broadly neutralizing antibody ACS202 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NCP
- Type
- protein
- Length
- 895 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACS202 Fab heavy chain; ACS202 Fab light chain; HIV-1 fusion peptide (residues 512-520)…
- Ligands
- GLY, SO4
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ACS202 Fab heavy chain | protein | 228 | 6% helix, 51% strand | — |
| B, D | ACS202 Fab light chain | protein | 212 | 6% helix, 52% strand | — |
| C | ACS202 Fab heavy chain | protein | 229 | 4% helix, 52% strand | — |
| E | HIV-1 fusion peptide (residues 512-520) | protein | 9 | 0% helix, 67% strand | — |
| F | His-tag of fusion peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.74 | 0.77 | 113 | empty |
| 2 | 796 | 0.67 | 0.74 | 74 | SO4 |
| 3 | 68 | 0.43 | 0.82 | 24 | empty |
| 4 | 99 | 0.41 | 0.77 | 20 | empty |
| 5 | 102 | 0.39 | 0.76 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1735 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1688 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 758 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 468 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 386 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6NCP · Crystal structure of HIV-1 broadly neutralizing antibody ACS202 · the same entry in another collection · chain B against B, 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 6NCP · PDBe 6NCP
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