MolNFT v1 · #89622 · protein
The X-ray crystal structure of full-length type II human plasminogen
4DUR: “The X-ray crystal structure of full-length type II human plasminogen”. X-ray diffraction, 6 ligands (BCT, NAG, GAL), 19 pockets (best druggability 0.68). MolNFT v1 #89622 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DUR
- Type
- protein
- Length
- 1,510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen
- EC
- 3.4.21.7
- UniProt
- P00747
- Ligands
- BCT, NAG, GAL, SIA, K, CL
- Pockets
- 19 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasminogen (EC 3.4.21.7) | protein | 756 | 5% helix, 25% strand | P00747 |
| B | Plasminogen (EC 3.4.21.7) | protein | 754 | 6% helix, 25% strand | P00747 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.68 | 0.79 | 45 | CL |
| 2 | 495 | 0.67 | 0.78 | 44 | CL |
| 3 | 405 | 0.66 | 0.80 | 61 | empty |
| 4 | 679 | 0.66 | 0.75 | 72 | CL |
| 5 | 267 | 0.63 | 0.81 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 1167 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 disulfide, 2 glycan (disulfide, O-glycosylation).
Compared structures
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 P00747
- Elsewhere: RCSB PDB 4DUR · PDBe 4DUR · UniProt P00747
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