MolNFT v1 · #83155 · protein
Structure of human monoclonal antibody E317 Fab
3W9D · Antibody Fab heavy chain: “Structure of human monoclonal antibody E317 Fab”. X-ray diffraction, 6 pockets (best druggability 0.79). MolNFT v1 #83155 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3W9D
- Type
- protein
- Length
- 845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab heavy chain; Antibody Fab light chain
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab heavy chain | protein | 209 | 8% helix, 51% strand | — |
| B | Antibody Fab light chain | protein | 212 | 8% helix, 53% strand | — |
| C | Antibody Fab heavy chain | protein | 211 | 6% helix, 53% strand | — |
| D | Antibody Fab light chain | protein | 213 | 6% helix, 49% strand | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.79 | 0.82 | 103 | empty |
| 2 | 226 | 0.62 | 0.82 | 31 | empty |
| 3 | 321 | 0.60 | 0.78 | 27 | empty |
| 4 | 55 | 0.38 | 0.80 | 16 | empty |
| 5 | 67 | 0.34 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1605 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1580 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1112 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 102 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3W9D · Structure of Human Monoclonal Antibody E317 Fab · 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 3W9D · PDBe 3W9D
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