MolNFT v1 · #142568 · protein
The crystal structure of mupain-1-ig in complex with mupa-spd at PH8.5
6A8G: “The crystal structure of mupain-1-ig in complex with mupa-spd at PH8.5”. X-ray diffraction, 3 ligands (ACE, PO4, NH2), 3 pockets (best druggability 0.51). MolNFT v1 #142568 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6A8G
- Type
- protein
- Length
- 509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mupain-1-ig; Urokinase-type plasminogen activator chain B
- EC
- 3.4.21.73
- UniProt
- P06869
- Ligands
- ACE, PO4, NH2
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, E | Mupain-1-ig | protein | 10 | 0% helix, 10% strand | — |
| A | Urokinase-type plasminogen activator chain B (EC 3.4.21.73) | protein | 245 | 12% helix, 39% strand | P06869 |
| B | Urokinase-type plasminogen activator chain B (EC 3.4.21.73) | protein | 244 | 11% helix, 39% strand | P06869 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains P, A, B, E
- PO4 · Phosphate ion · ion · 5 copies · chains P, A, B
- NH2 · Amino group · ion · 2 copies · chains P, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.51 | 0.75 | 27 | empty |
| 2 | 142 | 0.46 | 0.77 | 28 | empty |
| 3 | 50 | 0.26 | 0.74 | 16 | ACE |
Interfaces
3 interfaces between chains.
- P–A · 829 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 769 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 675 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6A8G · The crystal structure of muPAin-1-IG in complex with muPA-SPD at pH8.5 · the same entry in another collection · chain P against P, TM-score 1.00
- P06869 · AlphaFold monomer V2.0 prediction for urokinase-type plasminogen activator (P06869) · a predicted model of the same protein · chain B 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 P06869
- Elsewhere: RCSB PDB 6A8G · PDBe 6A8G · UniProt P06869
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