Research workbench
Zinc-ALPHA2-glycoprotein with a fluorescent dansyl C 11 fatty acid
Analyse Zinc-ALPHA2-glycoprotein with a fluorescent dansyl C 11 fatty acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R2U
- Type
- protein
- Length
- 1,633 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc-alpha-2-glycoprotein
- UniProt
- P25311
- Ligands
- 11D, SO4, AZI
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | Zinc-alpha-2-glycoprotein | protein | 272 | 25% helix, 43% strand | P25311 |
| B | Zinc-alpha-2-glycoprotein | protein | 273 | 25% helix, 42% strand | P25311 |
| E | Zinc-alpha-2-glycoprotein | protein | 272 | 25% helix, 43% strand | P25311 |
Ligands and binding sites
- 11D · 11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino) undecanoic acid · ligand · 8 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 14 copies · chains A, F, B, C, D, E
- AZI · Azide ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.88 | 0.91 | 88 | 11D |
| 2 | 517 | 0.82 | 0.88 | 46 | 11D |
| 3 | 170 | 0.77 | 0.93 | 23 | empty |
| 4 | 363 | 0.76 | 0.87 | 56 | empty |
| 5 | 271 | 0.61 | 0.79 | 19 | 11D |
Interfaces
11 interfaces between chains.
- A–D · 788 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 774 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 418 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 389 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 361 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6R2U · Zinc-alpha2-Glycoprotein with a Fluorescent Dansyl C 11 Fatty Acid · the same entry in another collection · chain F against F, TM-score 1.00
- P25311 · AlphaFold monomer V2.0 prediction for zinc-alpha-2-glycoprotein (P25311) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 P25311
- Elsewhere: RCSB PDB 6R2U · PDBe 6R2U · UniProt P25311
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