MolNFT v1 · #10992 · protein
Crystal structure of tissue factor-factor viia complex
1J9C: “Crystal structure of tissue factor-factor viia complex”. X-ray diffraction, 5 ligands (0Z6, GLC, FUL), 9 pockets (best druggability 0.68). MolNFT v1 #10992 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1J9C
- Type
- protein
- Length
- 559 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tissue factor; Factor viia light chain; Factor viia heavy chain
- UniProt
- P13726, P08709
- Ligands
- 0Z6, GLC, FUL, NAG, CA
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Tissue factor | protein | 210 | 7% helix, 40% strand | P13726 |
| L | Factor viia light chain | protein | 95 | 11% helix, 24% strand | P08709 |
| H | Factor viia heavy chain | protein | 254 | 13% helix, 36% strand | P08709 |
Ligands and binding sites
- 0Z6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide · ligand · chains H
- GLC · alpha-D-glucopyranose · sugar · chains L
- FUL · beta-L-fucopyranose · sugar · chains T, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- CA · Calcium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.68 | 0.84 | 35 | empty |
| 2 | 79 | 0.50 | 0.84 | 20 | empty |
| 3 | 173 | 0.50 | 0.77 | 21 | empty |
| 4 | 153 | 0.48 | 0.77 | 27 | empty |
| 5 | 105 | 0.47 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1039 Ų buried · 14 hydrogen bonds · protein-protein
- T–L · 986 Ų buried · 15 hydrogen bonds · protein-protein
- T–H · 698 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 3 glycan, 2 covalent (disulfide, covalent ligand, O-glycosylation, N-glycosylation).
Compared structures
- 1J9C · Crystal Structure of tissue factor-factor VIIa complex · the same entry in another collection · chain T against T, TM-score 1.00
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain H against A, TM-score 0.97
- P13726 · AlphaFold monomer V2.0 prediction for tissue factor (P13726) · a predicted model of the same protein · chain T against A, TM-score 0.95
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
- Every structure of UniProt P08709
- Elsewhere: RCSB PDB 1J9C · PDBe 1J9C · UniProt P13726 · UniProt P08709
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