Research workbench
Fab fragment of antiporphyrin antibody 14H7
Analyse Fab fragment of antiporphyrin antibody 14H7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AT6
- Type
- protein
- Length
- 3,356 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 14H7 heavy chain; Fab 14H7 light chain
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 8 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 14H7 heavy chain | protein | 212 | 6% helix, 42% strand | — |
| B, D, F, I, K, L, N, P | Fab 14H7 light chain | protein | 212 | 7% helix, 54% strand | — |
| C, E | Fab 14H7 heavy chain | protein | 209 | 3% helix, 45% strand | — |
| G | Fab 14H7 heavy chain | protein | 205 | 4% helix, 42% strand | — |
| H | Fab 14H7 heavy chain | protein | 211 | 3% helix, 43% strand | — |
| J | Fab 14H7 heavy chain | protein | 207 | 1% helix, 41% strand | — |
| M | Fab 14H7 heavy chain | protein | 203 | 1% helix, 48% strand | — |
| O | Fab 14H7 heavy chain | protein | 204 | 1% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.61 | 0.75 | 61 | empty |
| 2 | 439 | 0.60 | 0.75 | 60 | empty |
| 3 | 432 | 0.59 | 0.75 | 59 | empty |
| 4 | 412 | 0.58 | 0.75 | 55 | empty |
| 5 | 394 | 0.58 | 0.75 | 47 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1930 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1925 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1912 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1882 Ų buried · 9 hydrogen bonds · protein-protein
- G–I · 1852 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 4AT6 · Fab fragment of antiporphyrin antibody 14H7 · 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 4AT6 · PDBe 4AT6
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