MolNFT v1 · #93241 · protein
Crystal structure of human promeprin beta
4GWM · Meprin a subunit beta: “Crystal structure of human promeprin beta”. X-ray diffraction, 7 ligands (NAG, MAN, FUC), 13 pockets (best druggability 0.80). MolNFT v1 #93241 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GWM
- Type
- protein
- Length
- 1,115 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meprin a subunit beta
- EC
- 3.4.24.63
- UniProt
- Q16820
- Ligands
- NAG, MAN, FUC, BMA, ZN, NA, CL
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meprin a subunit beta (EC 3.4.24.63) | protein | 561 | 15% helix, 34% strand | Q16820 |
| B | Meprin a subunit beta (EC 3.4.24.63) | protein | 554 | 17% helix, 32% strand | Q16820 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.80 | 0.88 | 38 | empty |
| 2 | 440 | 0.80 | 0.88 | 37 | CL |
| 3 | 733 | 0.76 | 0.81 | 94 | CL |
| 4 | 322 | 0.71 | 0.84 | 33 | empty |
| 5 | 227 | 0.66 | 0.84 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1122 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 4 disulfide (N-glycosylation, disulfide).
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 Q16820
- Elsewhere: RCSB PDB 4GWM · PDBe 4GWM · UniProt Q16820
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