Research workbench
Crystal structure of human mature meprin beta in complex with the specific inhibitor mwt-S-270
Analyse Crystal structure of human mature meprin beta in complex with the specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AQ1
- Type
- protein
- Length
- 1,066 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meprin B subunit beta
- EC
- 3.4.24.63
- UniProt
- Q16820
- Ligands
- RUE, NAG, MAN, BMA, CA, ZN, CL
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Meprin B subunit beta (EC 3.4.24.63) | protein | 533 | 15% helix, 34% strand | Q16820 |
Ligands and binding sites
- RUE · 3-[[(3-Carboxyphenyl)methyl-[2-(hydroxyamino)-2-oxoethyl]amino]methyl]benzoic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.81 | 0.89 | 36 | CL |
| 2 | 439 | 0.79 | 0.87 | 36 | EDO, CL |
| 3 | 770 | 0.79 | 0.83 | 106 | EDO |
| 4 | 266 | 0.56 | 0.77 | 40 | ZN, EDO, RUE |
| 5 | 324 | 0.54 | 0.75 | 37 | ZN, EDO, RUE |
Interfaces
1 interface between chains.
- A–B · 1474 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7AQ1 · Crystal structure of human mature meprin beta in complex with the specific inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q16820 · AlphaFold monomer V2.0 prediction for meprin a subunit beta (Q16820) · a predicted model of the same protein · chain A 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 Q16820
- Elsewhere: RCSB PDB 7AQ1 · PDBe 7AQ1 · UniProt Q16820
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