MolNFT v1 · #175675 · protein
Crystal structure of CMD1 in complex with vitamin C
7CY5 · Maltodextrin-binding PROTEIN,5-methylcytosine-modifying…: “Crystal structure of CMD1 in complex with vitamin C”. X-ray diffraction, 2 ligands (ASC, FE), 9 pockets (best druggability 0.70). MolNFT v1 #175675 on GenesisL1: 3D…
- PDB
- 7CY5
- Type
- protein
- Length
- 862 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding PROTEIN,5-methylcytosine-modifying enzyme 1
- EC
- 1.14.99.-
- UniProt
- A0A376KDN7, A0A2K3D5Z7
- Ligands
- ASC, FE
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltodextrin-binding PROTEIN,5-methylcytosine-modifying enzyme 1 (EC 1.14.99.-) | protein | 862 | 43% helix, 23% strand | A0A376KDN7, A0A2K3D5Z7 |
Ligands and binding sites
- ASC · Ascorbic acid · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- CIT · Citric acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.70 | 0.84 | 34 | empty |
| 2 | 439 | 0.69 | 0.80 | 60 | empty |
| 3 | 193 | 0.63 | 0.83 | 36 | empty |
| 4 | 237 | 0.63 | 0.81 | 33 | FE, ASC |
| 5 | 361 | 0.59 | 0.76 | 47 | empty |
Compared structures
- 7CY5 · Crystal Structure of CMD1 in complex with vitamin C · 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 A0A376KDN7
- Every structure of UniProt A0A2K3D5Z7
- Elsewhere: RCSB PDB 7CY5 · PDBe 7CY5 · UniProt A0A376KDN7 · UniProt A0A2K3D5Z7
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