Research workbench
Structure of the unliganded Fab from HIV-1 neutralizing antibody CAP248-2B that binds to the GP120 C-terminus - GP41 interface, at two ångström resolution.
Analyse Structure of the unliganded Fab from HIV-1 neutralizing antibody CAP248-2B that… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MP6
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CAP248-2B heavy chain; CAP248-2B light chain
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | CAP248-2B heavy chain | protein | 211 | 4% helix, 46% strand | — |
| Q | CAP248-2B light chain | protein | 208 | 6% helix, 48% strand | — |
| H | CAP248-2B heavy chain | protein | 230 | 7% helix, 49% strand | — |
| L | CAP248-2B light chain | protein | 225 | 6% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains P, Q, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.86 | 0.87 | 133 | SO4 |
| 2 | 172 | 0.55 | 0.80 | 24 | empty |
| 3 | 101 | 0.55 | 0.85 | 23 | empty |
| 4 | 139 | 0.52 | 0.80 | 31 | empty |
| 5 | 184 | 0.51 | 0.77 | 24 | empty |
Interfaces
6 interfaces between chains.
- H–L · 2066 Ų buried · 17 hydrogen bonds · protein-protein
- P–Q · 1955 Ų buried · 19 hydrogen bonds · protein-protein
- Q–L · 509 Ų buried · 4 hydrogen bonds · protein-protein
- P–H · 463 Ų buried · 8 hydrogen bonds · protein-protein
- Q–H · 405 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 modified (disulfide, cyclization).
Compared structures
- 5MP6 · Structure of the Unliganded Fab from HIV-1 Neutralizing Antibody CAP248-2B that Binds to… · 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
- Elsewhere: RCSB PDB 5MP6 · PDBe 5MP6
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