Research workbench
Complex of benzamidine with the catalytic domain of human two chain tissue plasminogen activator [(tc)-T-pa]
Analyse Complex of benzamidine with the catalytic domain of human two chain tissue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RTF
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two chain tissue plasminogen activator
- EC
- 3.4.21.68
- UniProt
- P00750
- Ligands
- BEN, PO4
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Two chain tissue plasminogen activator (EC 3.4.21.68) | protein | 7 | 0% helix, 0% strand | — |
| B | Two chain tissue plasminogen activator (EC 3.4.21.68) | protein | 242 | 10% helix, 36% strand | P00750 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.52 | 0.79 | 25 | empty |
| 2 | 137 | 0.45 | 0.77 | 28 | PO4, BEN |
Interfaces
1 interface between chains.
- A–B · 478 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1RTF · Complex of benzamidine with the catalytic domain of human two chain tissue plasminogen… · the same entry in another collection · chain A against A, TM-score 1.00
- P00750 · AlphaFold monomer V2.0 prediction for tissue-type plasminogen activator (P00750) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P00750
- Elsewhere: RCSB PDB 1RTF · PDBe 1RTF · UniProt P00750
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