MolNFT v1 · #144554 · protein
Human mesotrypsin (PRSS3) complexed with tissue factor pathway inhibitor variant (TFPI1-KD1-K15R-I17C-I34C)
6BX8 · Trypsin-3: “Human mesotrypsin (PRSS3) complexed with tissue factor pathway inhibitor variant (TFPI1-KD1-K15R-I17C-I34C)”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.70). MolNFT v1 #144554 on GenesisL1: 3D…
- PDB
- 6BX8
- Type
- protein
- Length
- 1,113 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin-3; Tissue factor pathway inhibitor
- EC
- 3.4.21.4
- UniProt
- P35030, P10646
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Trypsin-3 (EC 3.4.21.4) | protein | 224 | 11% helix, 35% strand | P35030 |
| B, H | Tissue factor pathway inhibitor | protein | 55 | 20% helix, 29% strand | P10646 |
| D | Tissue factor pathway inhibitor | protein | 53 | 19% helix, 30% strand | P10646 |
| F | Tissue factor pathway inhibitor | protein | 54 | 20% helix, 30% strand | P10646 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.70 | 0.77 | 81 | empty |
| 2 | 201 | 0.57 | 0.80 | 28 | empty |
| 3 | 257 | 0.52 | 0.75 | 32 | empty |
| 4 | 123 | 0.39 | 0.74 | 23 | empty |
| 5 | 91 | 0.38 | 0.76 | 21 | empty |
Interfaces
9 interfaces between chains.
- E–F · 723 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 716 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 713 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 581 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 6BX8 · Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant… · the same entry in another collection · chain H against H, TM-score 1.00
- P35030 · AlphaFold monomer V2.0 prediction for trypsin-3 (P35030) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P10646 · AlphaFold monomer V2.0 prediction for tissue factor pathway inhibitor (P10646) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P35030
- Every structure of UniProt P10646
- Elsewhere: RCSB PDB 6BX8 · PDBe 6BX8 · UniProt P35030 · UniProt P10646
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