MolNFT v1 · #137835 · protein + DNA
Crystal structure of mbp fused activation-induced cytidine deaminase (aid) in complex with dcmp
5W0U · Maltose-binding periplasmic PROTEIN,SINGLE-stranded DNA…: “Crystal structure of mbp fused activation-induced cytidine deaminase (aid) in complex with dcmp”. X-ray diffraction, 3 ligands (DCM, ZN, CA), 14 pockets (best druggability…
- PDB
- 5W0U
- Type
- protein + DNA
- Length
- 1,108 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,SINGLE-stranded DNA cytosine deaminase; DNA…
- EC
- 3.5.4.38
- UniProt
- P0AEY0, Q9GZX7
- Ligands
- DCM, ZN, CA
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Maltose-binding periplasmic PROTEIN,SINGLE-stranded DNA cytosine deaminase (EC 3.5.4.38) | protein | 542 | 43% helix, 19% 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
- DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
- GOL · Glycerol · additive · chains B
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 | 719 | 0.66 | 0.74 | 76 | empty |
| 2 | 193 | 0.64 | 0.84 | 24 | empty |
| 3 | 466 | 0.61 | 0.75 | 56 | CA |
| 4 | 192 | 0.59 | 0.82 | 30 | empty |
| 5 | 454 | 0.59 | 0.74 | 54 | empty |
Interfaces
4 interfaces between chains.
- D–G · 535 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–A · 436 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 294 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–D · 202 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5W0U · 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 5W0U · PDBe 5W0U · UniProt P0AEY0 · UniProt Q9GZX7
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