MolNFT v1 · #1557 · protein
Dcmp hydroxymethylase from T4 (intact)
1B5D · Protein (deoxycytidylate hydroxymethylase): “Dcmp hydroxymethylase from T4 (intact)”. X-ray diffraction, 1 ligand (DCM), 2 pockets (best druggability 0.77). MolNFT v1 #1557 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1B5D
- Type
- protein
- Length
- 492 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (deoxycytidylate hydroxymethylase)
- EC
- 2.1.2.8
- UniProt
- P08773
- Ligands
- DCM
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (deoxycytidylate hydroxymethylase) (EC 2.1.2.8) | protein | 246 | 40% helix, 23% strand | P08773 |
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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.77 | 0.86 | 36 | DCM |
| 2 | 469 | 0.75 | 0.84 | 41 | DCM |
Interfaces
1 interface between chains.
- A–B · 2683 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 1B5D · DCMP Hydroxymethylase from T4 (Intact) · 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 P08773
- Elsewhere: RCSB PDB 1B5D · PDBe 1B5D · UniProt P08773
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