Research workbench
Crystal structure of yjjv, tatd homolog from escherichia COLI K12, at 1.8 a resolution
Analyse Crystal structure of yjjv, tatd homolog from escherichia COLI K12, at 1.8 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZZM
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative deoxyribonuclease yjjv
- EC
- 3.1.21.-
- UniProt
- P39408
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative deoxyribonuclease yjjv (EC 3.1.21.-) | protein | 259 | 47% helix, 17% strand | P39408 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.33 | 0.75 | 14 | empty |
Compared structures
- 1ZZM · Crystal structure of YJJV, TATD Homolog from Escherichia coli k12, at 1.8 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P39408 · AlphaFold monomer V2.0 prediction for uncharacterized metal-dependent hydrolase yjjv… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P39408
- Elsewhere: RCSB PDB 1ZZM · PDBe 1ZZM · UniProt P39408
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