MolNFT v1 · #123414 · protein
Crystal structure of a variant human activation-induced deoxycytidine deaminase as an mbp fusion protein
5JJ4 · Maltose-binding periplasmic PROTEIN,SINGLE-stranded DNA…: “Crystal structure of a variant human activation-induced deoxycytidine deaminase as an mbp fusion protein”. X-ray diffraction, 3 ligands (GLC, ZN, CA), 15 pockets (best…
- PDB
- 5JJ4
- Type
- protein
- Length
- 1,628 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,SINGLE-stranded DNA cytosine deaminase
- EC
- 3.5.4.38
- UniProt
- P0AEY0, Q9GZX7
- Ligands
- GLC, ZN, CA
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Maltose-binding periplasmic PROTEIN,SINGLE-stranded DNA cytosine deaminase (EC 3.5.4.38) | protein | 541 | 43% helix, 21% strand | P0AEY0, Q9GZX7 |
| A | Maltose-binding periplasmic PROTEIN,SINGLE-stranded DNA cytosine deaminase (EC 3.5.4.38) | protein | 542 | 43% helix, 22% strand | P0AEY0, Q9GZX7 |
| B | Maltose-binding periplasmic PROTEIN,SINGLE-stranded DNA cytosine deaminase (EC 3.5.4.38) | protein | 545 | 43% helix, 19% strand | P0AEY0, Q9GZX7 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains C, A, B
- ZN · Zinc ion · metal · 3 copies · chains C, A, B
- CA · Calcium ion · metal · 3 copies · chains C, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.79 | 0.80 | 88 | empty |
| 2 | 401 | 0.73 | 0.83 | 32 | GLC |
| 3 | 426 | 0.72 | 0.82 | 35 | GLC |
| 4 | 334 | 0.71 | 0.83 | 30 | GLC |
| 5 | 284 | 0.61 | 0.79 | 36 | empty |
Interfaces
2 interfaces between chains.
- C–B · 833 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 337 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5JJ4 · Crystal Structure of a Variant Human Activation-induced Deoxycytidine Deaminase as an MBP… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9GZX7 · AlphaFold monomer V2.0 prediction for single-stranded DNA cytosine deaminase (Q9GZX7) · a predicted model of the same protein · chain B against A, TM-score 0.32
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 P0AEY0
- Every structure of UniProt Q9GZX7
- Elsewhere: RCSB PDB 5JJ4 · PDBe 5JJ4 · UniProt P0AEY0 · UniProt Q9GZX7
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