MolNFT v1 · #84822 · protein
The 3-dimensional structure of mpgp from thermus thermophilus HB27, in complex with the alpha-mannosylglycerate.
3ZWD · Mannosyl-3-phosphoglycerate phosphatase: “The 3-dimensional structure of mpgp from thermus thermophilus HB27, in complex with the…”. X-ray diffraction, 2 ligands (2M8, MG), 5 pockets (best druggability 0.67). MolNFT v1 #84822 on…
- PDB
- 3ZWD
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannosyl-3-phosphoglycerate phosphatase
- EC
- 3.1.3.70
- UniProt
- Q72K29
- Ligands
- 2M8, MG
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 251 | 41% helix, 20% strand | Q72K29 |
| B | Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70) | protein | 252 | 44% helix, 20% strand | Q72K29 |
Ligands and binding sites
- 2M8 · (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.67 | 0.82 | 47 | 2M8 |
| 2 | 241 | 0.65 | 0.83 | 39 | 2M8 |
| 3 | 145 | 0.61 | 0.84 | 25 | empty |
| 4 | 125 | 0.42 | 0.75 | 22 | empty |
| 5 | 55 | 0.33 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 791 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3ZWD · The 3-dimensional structure of MpgP from Thermus thermophilus HB27, in complex with the… · 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 Q72K29
- Elsewhere: RCSB PDB 3ZWD · PDBe 3ZWD · UniProt Q72K29
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