MolNFT v1 · #191367 · protein
The structure of the 'alt' construct of the AMUC_1438 glycopeptidase
8DF2 · NPCBM/NEW2 domain-containing protein: “The structure of the 'alt' construct of the AMUC_1438 glycopeptidase”. X-ray diffraction, 3 ligands (NA, ZN, CA), 11 pockets (best druggability 0.74). MolNFT v1 #191367 on GenesisL1: 3D…
- PDB
- 8DF2
- Type
- protein
- Length
- 1,496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NPCBM/NEW2 domain-containing protein
- UniProt
- A0A8F1DJZ3
- Ligands
- NA, ZN, CA
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NPCBM/NEW2 domain-containing protein | protein | 374 | 28% helix, 28% strand | A0A8F1DJZ3 |
| B | NPCBM/NEW2 domain-containing protein | protein | 374 | 28% helix, 28% strand | A0A8F1DJZ3 |
| C | NPCBM/NEW2 domain-containing protein | protein | 374 | 27% helix, 28% strand | A0A8F1DJZ3 |
Ligands and binding sites
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.74 | 0.85 | 29 | empty |
| 2 | 406 | 0.69 | 0.81 | 29 | empty |
| 3 | 759 | 0.68 | 0.75 | 70 | empty |
| 4 | 707 | 0.67 | 0.75 | 65 | empty |
| 5 | 736 | 0.66 | 0.75 | 64 | empty |
Interfaces
6 interfaces between chains.
- A–B · 797 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 795 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 453 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 426 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 8DF2 · The structure of the 'ALT' construct of the Amuc_1438 glycopeptidase · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A8F1DJZ3
- Elsewhere: RCSB PDB 8DF2 · PDBe 8DF2 · UniProt A0A8F1DJZ3
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