MolNFT v1 · #13763 · protein
Lmw U-pa structure complexed with egrcmk (glu-gly-arg chloromethyl ketone)
1LMW · Urokinase-type plasminogen activator: “Lmw U-pa structure complexed with egrcmk (glu-gly-arg chloromethyl ketone)”. X-ray diffraction, 1 ligand (0GJ), 2 pockets (best druggability 0.77). MolNFT v1 #13763 on GenesisL1: 3D structure…
- PDB
- 1LMW
- Type
- protein
- Length
- 512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- 0GJ
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 8 | 0% helix, 0% strand | P00749 |
| B, D | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 248 | 9% helix, 33% strand | P00749 |
Ligands and binding sites
- 0GJ · L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide · ligand · 2 copies · chains B, D
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 | 908 | 0.77 | 0.80 | 89 | 0GJ |
| 2 | 61 | 0.40 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 523 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 508 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 444 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 1LMW · LMW U-PA Structure complexed with EGRCMK (GLU-GLY-ARG Chloromethyl Ketone) · the same entry in another collection · chain D against D, TM-score 1.00
- P00749 · AlphaFold monomer V2.0 prediction for urokinase-type plasminogen activator (P00749) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P00749
- Elsewhere: RCSB PDB 1LMW · PDBe 1LMW · UniProt P00749
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