MolNFT v1 · #163709 · protein
Cleaved human fetuin-B in complex with crayfish astacin
6SAZ: “Cleaved human fetuin-B in complex with crayfish astacin”. X-ray diffraction, 4 ligands (NAG, BMA, FUC), 7 pockets (best druggability 0.68). MolNFT v1 #163709 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SAZ
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Astacin; Fetuin-B
- EC
- 3.4.24.21
- UniProt
- P07584, Q9UGM5
- Ligands
- NAG, BMA, FUC, ZN
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Astacin (EC 3.4.24.21) | protein | 199 | 30% helix, 19% strand | P07584 |
| B | Fetuin-B | protein | 234 | 18% helix, 44% strand | Q9UGM5 |
| C | Astacin (EC 3.4.24.21) | protein | 200 | 32% helix, 19% strand | P07584 |
| D | Fetuin-B | protein | 231 | 21% helix, 45% strand | Q9UGM5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains D
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.68 | 0.80 | 73 | empty |
| 2 | 278 | 0.64 | 0.81 | 44 | empty |
| 3 | 361 | 0.64 | 0.79 | 50 | empty |
| 4 | 92 | 0.41 | 0.77 | 13 | empty |
| 5 | 109 | 0.39 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1526 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1381 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 128 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6SAZ · Cleaved human fetuin-b in complex with crayfish astacin · the same entry in another collection · chain D against D, TM-score 1.00
- P07584 · AlphaFold monomer V2.0 prediction for astacin (P07584) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UGM5 · AlphaFold monomer V2.0 prediction for fetuin-B (Q9UGM5) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P07584
- Every structure of UniProt Q9UGM5
- Elsewhere: RCSB PDB 6SAZ · PDBe 6SAZ · UniProt P07584 · UniProt Q9UGM5
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