Research workbench
Human tissue factor in complex with antibody M1587
Analyse Human tissue factor in complex with antibody M1587 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W06
- Type
- protein
- Length
- 633 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tissue factor; M1587 Fab light chain; M1587 Fab heavy chain
- UniProt
- P13726
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Tissue factor | protein | 198 | 8% helix, 50% strand | P13726 |
| L | M1587 Fab light chain | protein | 219 | 6% helix, 51% strand | — |
| H | M1587 Fab heavy chain | protein | 216 | 5% helix, 52% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.60 | 0.76 | 43 | empty |
| 2 | 96 | 0.45 | 0.79 | 24 | empty |
| 3 | 127 | 0.41 | 0.75 | 29 | empty |
| 4 | 119 | 0.38 | 0.74 | 25 | empty |
| 5 | 107 | 0.36 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1862 Ų buried · 19 hydrogen bonds · protein-protein
- T–H · 764 Ų buried · 12 hydrogen bonds · protein-protein
- T–L · 474 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5W06 · Human tissue factor in complex with antibody M1587 · the same entry in another collection · chain T against T, 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
- Every structure of UniProt P13726
- Elsewhere: RCSB PDB 5W06 · PDBe 5W06 · UniProt P13726
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