Research workbench
Crystal structure of cytidine monophosphate hydroxymethylase mila with dcmp
Analyse Crystal structure of cytidine monophosphate hydroxymethylase mila with dcmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JP9
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cmp 5-hydroxymethylase
- UniProt
- B4Y380
- Ligands
- DCM
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cmp 5-hydroxymethylase | protein | 317 | 48% helix, 18% strand | B4Y380 |
| B | Cmp 5-hydroxymethylase | protein | 318 | 48% helix, 18% strand | B4Y380 |
Ligands and binding sites
- DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.76 | 0.84 | 47 | DCM |
| 2 | 632 | 0.76 | 0.82 | 60 | DCM |
| 3 | 190 | 0.53 | 0.78 | 35 | empty |
| 4 | 82 | 0.36 | 0.76 | 21 | empty |
| 5 | 80 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2220 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5JP9 · Crystal Structure of cytidine monophosphate hydroxymethylase MilA with dCMP · 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 B4Y380
- Elsewhere: RCSB PDB 5JP9 · PDBe 5JP9 · UniProt B4Y380
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