Research workbench
Crystal structure of mbp fused activation-induced cytidine deaminase (aid) in complex with cacodylic acid
Analyse Crystal structure of mbp fused activation-induced cytidine deaminase (aid) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W0R
- Type
- protein
- Length
- 1,090 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mbp fused activation-induced cytidine deaminase
- EC
- 3.5.4.38
- UniProt
- P0AEY0, Q9GZX7
- Ligands
- ZN, CA
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mbp fused activation-induced cytidine deaminase (EC 3.5.4.38) | protein | 542 | 42% helix, 20% strand | P0AEY0, Q9GZX7 |
| A | Mbp fused activation-induced cytidine deaminase (EC 3.5.4.38) | protein | 548 | 42% helix, 20% strand | P0AEY0, Q9GZX7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
- CAC · Cacodylate ion · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.75 | 0.80 | 79 | empty |
| 2 | 570 | 0.68 | 0.78 | 56 | empty |
| 3 | 225 | 0.57 | 0.79 | 33 | empty |
| 4 | 75 | 0.57 | 0.88 | 18 | empty |
| 5 | 72 | 0.56 | 0.88 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 1451 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5W0R · Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex… · the same entry in another collection · chain B against B, 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 A 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 5W0R · PDBe 5W0R · UniProt P0AEY0 · UniProt Q9GZX7
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