Research workbench
Crystal structure of catalytic domain of anhydrobiosis-related mn- dependent peroxidase (amnp) from ramazzottius varieornatus (ZN2+- bound form)
Analyse Crystal structure of catalytic domain of anhydrobiosis-related mn- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DBU
- Type
- protein
- Length
- 319 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMNP/G12777
- UniProt
- A0A1D1VPD8
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMNP/G12777 | protein | 161 | 7% helix, 45% strand | A0A1D1VPD8 |
| B | AMNP/G12777 | protein | 158 | 8% helix, 46% strand | A0A1D1VPD8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.57 | 0.77 | 48 | ZN |
Interfaces
1 interface between chains.
- A–B · 347 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7DBU · Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase… · the same entry in another collection · chain A against A, 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 A0A1D1VPD8
- Elsewhere: RCSB PDB 7DBU · PDBe 7DBU · UniProt A0A1D1VPD8
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