MolNFT v1 · #114234 · protein
Crystal structure of cytidine monophosphate hydroxymethylase mila with hmcmp
5B6E · Cmp 5-hydroxymethylase: “Crystal structure of cytidine monophosphate hydroxymethylase mila with hmcmp”. X-ray diffraction, 1 ligand (5HM), 7 pockets (best druggability 0.76). MolNFT v1 #114234 on GenesisL1: 3D structure, binding…
- PDB
- 5B6E
- Type
- protein
- Length
- 637 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cmp 5-hydroxymethylase
- UniProt
- B4Y380
- Ligands
- 5HM
- Pockets
- 7 · 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 | 319 | 48% helix, 18% strand | B4Y380 |
| B | Cmp 5-hydroxymethylase | protein | 318 | 48% helix, 18% strand | B4Y380 |
Ligands and binding sites
- 5HM · 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.76 | 0.83 | 51 | 5HM |
| 2 | 479 | 0.75 | 0.84 | 47 | 5HM |
| 3 | 231 | 0.55 | 0.78 | 37 | empty |
| 4 | 105 | 0.41 | 0.77 | 16 | empty |
| 5 | 103 | 0.40 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2204 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5B6E · Crystal Structure of cytidine monophosphate hydroxymethylase MilA with hmCMP · 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 5B6E · PDBe 5B6E · UniProt B4Y380
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.