Research workbench
Crystal structure of MSMEG3575 in complex with ammeline
Analyse Crystal structure of MSMEG3575 in complex with ammeline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XKQ
- Type
- protein
- Length
- 619 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
- 6AM, ZN
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CMP/DCMP deaminase, zinc-binding protein | protein | 154 | 49% helix, 16% strand | A0QY90 |
| B, D | CMP/DCMP deaminase, zinc-binding protein | protein | 155 | 49% helix, 15% strand | A0QY90 |
| C | CMP/DCMP deaminase, zinc-binding protein | protein | 155 | 48% helix, 15% strand | A0QY90 |
Ligands and binding sites
- 6AM · 4,6-diamino-1,3,5-triazin-2-ol · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains 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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.67 | 0.88 | 29 | 6AM |
| 2 | 178 | 0.66 | 0.86 | 34 | 6AM |
| 3 | 136 | 0.65 | 0.87 | 27 | 6AM, GOL |
| 4 | 197 | 0.65 | 0.84 | 32 | 6AM |
| 5 | 380 | 0.61 | 0.77 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1083 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1053 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 323 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5XKQ · Crystal structure of Msmeg3575 in complex with ammeline · 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 5XKQ · PDBe 5XKQ · UniProt A0QY90
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