MolNFT v1 · #140184 · protein
A human antibody AF4H1L1
5Y2K · A group 2 ha binding antibody AF4H1K1 Fab heavy chain: “A human antibody AF4H1L1”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #140184 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y2K
- Type
- protein
- Length
- 1,714 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A group 2 ha binding antibody AF4H1K1 Fab heavy chain; A group 2 ha binding antibody…
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | A group 2 ha binding antibody AF4H1K1 Fab heavy chain | protein | 223 | 8% helix, 49% strand | — |
| B, D, F, H | A group 2 ha binding antibody AF4H1K1 Fab light chain | protein | 208 | 8% helix, 51% strand | — |
| C | A group 2 ha binding antibody AF4H1K1 Fab heavy chain | protein | 216 | 8% helix, 50% strand | — |
| G | A group 2 ha binding antibody AF4H1K1 Fab heavy chain | protein | 220 | 7% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.75 | 0.81 | 83 | empty |
| 2 | 924 | 0.75 | 0.78 | 109 | empty |
| 3 | 575 | 0.68 | 0.78 | 63 | empty |
| 4 | 612 | 0.64 | 0.75 | 66 | empty |
| 5 | 571 | 0.61 | 0.74 | 66 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1877 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1817 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1776 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1732 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 547 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5Y2K · A human antibody AF4H1L1 · the same entry in another collection · chain A against A, 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 5Y2K · PDBe 5Y2K
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