MolNFT v1 · #142329 · protein
Crystal structure of broadly neutralizing antibody 13D4
6A0X · Antibody 13D4, Fab heavy chain: “Crystal structure of broadly neutralizing antibody 13D4”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #142329 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6A0X
- Type
- protein
- Length
- 1,752 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 13D4, Fab heavy chain; Antibody 13D4, Fab light chain
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Antibody 13D4, Fab heavy chain | protein | 224 | 7% helix, 50% strand | — |
| B, D, F, H | Antibody 13D4, Fab light chain | protein | 214 | 6% helix, 52% strand | — |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.76 | 0.79 | 120 | empty |
| 2 | 407 | 0.62 | 0.78 | 48 | empty |
| 3 | 316 | 0.54 | 0.75 | 52 | empty |
| 4 | 233 | 0.54 | 0.77 | 35 | empty |
| 5 | 278 | 0.53 | 0.75 | 53 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2020 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1996 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1974 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1951 Ų buried · 15 hydrogen bonds · protein-protein
- C–G · 401 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 modified (disulfide, cyclization).
Compared structures
- 6A0X · Crystal structure of broadly neutralizing antibody 13D4 · 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 6A0X · PDBe 6A0X
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