Research workbench
Crystal structure of milb E103A in complex with 5- hydroxymethylcytidine 5'-monophosphate (hmcmp) from streptomyces rimofaciens
Analyse Crystal structure of milb E103A in complex with 5- hydroxymethylcytidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OHB
- Type
- protein
- Length
- 159 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CMP/HYDROXYMETHYL cmp hydrolase
- UniProt
- B4Y381
- Ligands
- 5HM
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CMP/HYDROXYMETHYL cmp hydrolase | protein | 159 | 47% helix, 16% strand | B4Y381 |
Ligands and binding sites
- 5HM · 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.61 | 0.82 | 28 | 5HM |
| 2 | 78 | 0.37 | 0.77 | 20 | empty |
Compared structures
- 4OHB · Crystal structure of MilB E103A in complex with 5-hydroxymethylcytidine 5'-monophosphate… · 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 B4Y381
- Elsewhere: RCSB PDB 4OHB · PDBe 4OHB · UniProt B4Y381
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