MolNFT v1 · #89578 · protein
Hemostatic effect of a monoclonal antibody mab 2021 blocking the interaction between fxa and tfpi in a rabbit hemophilia model
4DTG · Humanized recombinant Fab fragment, Fab 2021, of a murine…: “Hemostatic effect of a monoclonal antibody mab 2021 blocking the interaction between fxa and tfpi in a rabbit…”. X-ray diffraction, 6 pockets (best druggability 0.81).…
- PDB
- 4DTG
- Type
- protein
- Length
- 500 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Humanized recombinant Fab fragment, Fab 2021, of a murine antibody, light chain…
- UniProt
- P10646
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Humanized recombinant Fab fragment, Fab 2021, of a murine antibody, light chain | protein | 219 | 5% helix, 50% strand | — |
| H | Humanized recombinant Fab fragment, Fab 2021, of a murine antibody, heavy chain | protein | 221 | 8% helix, 49% strand | — |
| K | Tissue factor pathway inhibitor | protein | 60 | 20% helix, 25% strand | P10646 |
Ligands and binding sites
- GOL · Glycerol · additive · 10 copies · chains L, H
- PGE · Triethylene glycol · additive · 3 copies · chains L, H, K
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 278 | 0.81 | 0.92 | 33 | PGE |
| 2 | 760 | 0.67 | 0.75 | 65 | PGE, GOL |
| 3 | 120 | 0.50 | 0.80 | 19 | empty |
| 4 | 102 | 0.36 | 0.74 | 26 | GOL |
| 5 | 85 | 0.33 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1924 Ų buried · 18 hydrogen bonds · protein-protein
- H–K · 735 Ų buried · 20 hydrogen bonds · protein-protein
- L–K · 340 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4DTG · Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa… · the same entry in another collection · chain L against L, TM-score 1.00
- P10646 · AlphaFold monomer V2.0 prediction for tissue factor pathway inhibitor (P10646) · a predicted model of the same protein · chain K 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 P10646
- Elsewhere: RCSB PDB 4DTG · PDBe 4DTG · UniProt P10646
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