Research workbench
Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor
Analyse Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UJ3
- Type
- protein
- Length
- 636 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG Fab light chain; IgG Fab heavy chain; Tissue factor
- UniProt
- P13726
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IgG Fab light chain | protein | 214 | 6% helix, 50% strand | — |
| B | IgG Fab heavy chain | protein | 217 | 6% helix, 52% strand | — |
| C | Tissue factor | protein | 205 | 8% helix, 48% strand | P13726 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.58 | 0.87 | 20 | empty |
| 2 | 404 | 0.57 | 0.74 | 53 | empty |
| 3 | 143 | 0.47 | 0.77 | 19 | empty |
| 4 | 50 | 0.46 | 0.86 | 23 | empty |
| 5 | 148 | 0.42 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1809 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 741 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1UJ3 · Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P13726 · AlphaFold monomer V2.0 prediction for tissue factor (P13726) · a predicted model of the same protein · chain C against A, TM-score 0.93
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P13726
- Elsewhere: RCSB PDB 1UJ3 · PDBe 1UJ3 · UniProt P13726
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