MolNFT v1 · #120668 · protein
Crystal structure of human mnda pyd domain with mbp tag
5H7Q: “Crystal structure of human mnda pyd domain with mbp tag”. X-ray diffraction, 1 ligand (GLC), 4 pockets (best druggability 0.70). MolNFT v1 #120668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H7Q
- Type
- protein
- Length
- 469 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mnda pyd domain with mbp tag
- Ligands
- GLC
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mnda pyd domain with mbp tag | protein | 469 | 54% helix, 17% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.70 | 0.84 | 32 | GLC |
| 2 | 556 | 0.68 | 0.78 | 51 | empty |
| 3 | 66 | 0.41 | 0.80 | 16 | empty |
| 4 | 125 | 0.38 | 0.73 | 25 | ACT |
Compared structures
- 5H7Q · Crystal structure of human MNDA PYD domain with MBP tag · 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
- Elsewhere: RCSB PDB 5H7Q · PDBe 5H7Q
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