MolNFT v1 · #125123 · protein
Structure of the HCV1-C1 antibody-antigen complex
5KZP · HCV1-C1 antibody Fab heavy chain: “Structure of the HCV1-C1 antibody-antigen complex”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.59). MolNFT v1 #125123 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5KZP
- Type
- protein
- Length
- 1,811 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HCV1-C1 antibody Fab heavy chain; HCV1-C1 antibody Fab light chain; C1 epitope
- Ligands
- CA
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, E, F, G | HCV1-C1 antibody Fab heavy chain | protein | 226 | 5% helix, 52% strand | — |
| L, I, J | HCV1-C1 antibody Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| A, B, C, D | C1 epitope | protein | 15 | 0% helix, 73% strand | — |
| K | HCV1-C1 antibody Fab light chain | protein | 211 | 6% helix, 51% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 21 copies · chains H, L, A, B, E, I, F, J, C, G, K
- ACT · Acetate ion · additive · 4 copies · chains H, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.59 | 0.75 | 53 | empty |
| 2 | 174 | 0.59 | 0.82 | 31 | empty |
| 3 | 210 | 0.58 | 0.80 | 31 | empty |
| 4 | 382 | 0.56 | 0.74 | 43 | empty |
| 5 | 366 | 0.54 | 0.73 | 50 | empty |
Interfaces
31 interfaces between chains.
- F–J · 1985 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1973 Ų buried · 18 hydrogen bonds · protein-protein
- E–I · 1908 Ų buried · 21 hydrogen bonds · protein-protein
- G–K · 1782 Ų buried · 18 hydrogen bonds · protein-protein
- F–C · 441 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5KZP · Structure of the HCV1-C1 Antibody-Antigen Complex · the same entry in another collection · chain H against H, 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 5KZP · PDBe 5KZP
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