MolNFT v1 · #151619 · protein
Mouse fetuin-B in complex with crayfish astacin
6HT9: “Mouse fetuin-B in complex with crayfish astacin”. X-ray diffraction, 2 ligands (NAG, ZN), 15 pockets (best druggability 0.76). MolNFT v1 #151619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HT9
- Type
- protein
- Length
- 1,015 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, Q9QXC1
- Ligands
- NAG, ZN
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Astacin (EC 3.4.24.21) | protein | 202 | 32% helix, 18% strand | P07584 |
| B | Fetuin-B | protein | 316 | 16% helix, 37% strand | Q9QXC1 |
| C | Astacin (EC 3.4.24.21) | protein | 200 | 32% helix, 19% strand | P07584 |
| D | Fetuin-B | protein | 297 | 19% helix, 38% strand | Q9QXC1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.76 | 0.82 | 86 | empty |
| 2 | 201 | 0.75 | 0.91 | 43 | empty |
| 3 | 256 | 0.62 | 0.81 | 35 | empty |
| 4 | 234 | 0.57 | 0.79 | 27 | empty |
| 5 | 242 | 0.56 | 0.78 | 35 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1269 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 712 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6HT9 · Mouse 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 C against A, TM-score 0.97
- Q9QXC1 · AlphaFold monomer V2.0 prediction for fetuin-B (Q9QXC1) · 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 Q9QXC1
- Elsewhere: RCSB PDB 6HT9 · PDBe 6HT9 · UniProt P07584 · UniProt Q9QXC1
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