MolNFT v1 · #137853 · protein + DNA
Crystal structure of mbp fused activation-induced cytidine deaminase (aid) in complex with cytidine
5W1C: “Crystal structure of mbp fused activation-induced cytidine deaminase (aid) in complex with cytidine”. X-ray diffraction, 3 ligands (CTN, ZN, CA), 12 pockets (best druggability 0.68). MolNFT v1 #137853 on GenesisL1: 3D structure…
- PDB
- 5W1C
- Type
- protein + DNA
- Length
- 1,110 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mbp fused activation-induced cytidine deaminase; DNA…
- EC
- 3.5.4.38
- UniProt
- P0AEY0, Q9GZX7
- Ligands
- CTN, ZN, CA
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Mbp fused activation-induced cytidine deaminase (EC 3.5.4.38) | protein | 543 | 43% helix, 20% strand | P0AEY0, Q9GZX7 |
| D | DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3') | dna | 12 | — | — |
| G | DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.68 | 0.77 | 79 | CA |
| 2 | 272 | 0.68 | 0.83 | 37 | CTN |
| 3 | 757 | 0.67 | 0.75 | 75 | empty |
| 4 | 458 | 0.59 | 0.74 | 47 | empty |
| 5 | 245 | 0.52 | 0.76 | 33 | empty |
Interfaces
4 interfaces between chains.
- D–G · 531 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- B–A · 368 Ų buried · 1 hydrogen bond · protein-protein
- B–G · 250 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–D · 188 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5W1C · 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 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 5W1C · PDBe 5W1C · UniProt P0AEY0 · UniProt Q9GZX7
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