Research workbench
Crystal structure of MSMEG3575 in complex with 5-azacytosine
Analyse Crystal structure of MSMEG3575 in complex with 5-azacytosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XKP
- Type
- protein
- Length
- 630 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CMP/DCMP deaminase, zinc-binding protein
- UniProt
- A0QY90
- Ligands
- 5AZ, ZN
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | CMP/DCMP deaminase, zinc-binding protein | protein | 157 | 48% helix, 16% strand | A0QY90 |
| B, D | CMP/DCMP deaminase, zinc-binding protein | protein | 158 | 47% helix, 16% strand | A0QY90 |
Ligands and binding sites
- 5AZ · 6-amino-1,3,5-triazin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.67 | 0.86 | 31 | 5AZ, GOL |
| 2 | 175 | 0.67 | 0.86 | 30 | 5AZ, GOL |
| 3 | 144 | 0.65 | 0.87 | 29 | 5AZ, GOL |
| 4 | 177 | 0.65 | 0.85 | 32 | 5AZ, GOL |
| 5 | 569 | 0.64 | 0.76 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1112 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1102 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 196 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XKP · Crystal structure of Msmeg3575 in complex with 5-azacytosine · the same entry in another collection · chain A against A, TM-score 1.00
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 A0QY90
- Elsewhere: RCSB PDB 5XKP · PDBe 5XKP · UniProt A0QY90
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