MolNFT v1 · #97690 · protein
Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase mgp complexed with PO4
4KMI: “Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase mgp complexed with PO4”. X-ray diffraction, 1 ligand (PO4), 9 pockets (best druggability 0.50). MolNFT v1 #97690 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4KMI
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-O-beta-D-mannosyl-D-glucose phosphorylase
- EC
- 2.4.1.281
- UniProt
- Q5LH68
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-O-beta-D-mannosyl-D-glucose phosphorylase (EC 2.4.1.281) | protein | 381 | 16% helix, 41% strand | Q5LH68 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.50 | 0.81 | 21 | empty |
| 2 | 74 | 0.49 | 0.84 | 19 | empty |
| 3 | 149 | 0.47 | 0.77 | 22 | empty |
| 4 | 137 | 0.46 | 0.77 | 19 | empty |
| 5 | 100 | 0.40 | 0.76 | 18 | MPD |
Interfaces
1 interface between chains.
- A–B · 335 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4KMI · Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with PO4 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5LH68 · AlphaFold monomer V2.0 prediction for 4-O-beta-D-mannosyl-D-glucose phosphorylase (Q5LH68) · a predicted model of the same protein · 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 Q5LH68
- Elsewhere: RCSB PDB 4KMI · PDBe 4KMI · UniProt Q5LH68
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