Research workbench
Cryo-EM structures of human GMPPA/GMPPB complex bound to GDP-mannose
Analyse Cryo-EM structures of human GMPPA/GMPPB complex bound to GDP-mannose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D72
- Type
- protein
- Length
- 4,505 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-1-phosphate guanyltransferase beta; Mannose-1-phosphate guanyltransferase alpha
- EC
- 2.7.7.13
- UniProt
- Q9Y5P6, Q96IJ6
- Ligands
- GDD, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, I, E, F, G, H, J, L | Mannose-1-phosphate guanyltransferase beta (EC 2.7.7.13) | protein | 360 | 25% helix, 28% strand | Q9Y5P6 |
| A | Mannose-1-phosphate guanyltransferase alpha | protein | 407 | 22% helix, 29% strand | Q96IJ6 |
| B, C, D | Mannose-1-phosphate guanyltransferase alpha | protein | 406 | 24% helix, 29% strand | Q96IJ6 |
Ligands and binding sites
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 12 copies · chains K, I, A, B, C, D, E, F, G, H, J, L
- MG · Magnesium ion · metal · 3 copies · chains E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.79 | 0.82 | 81 | GDD |
| 2 | 188 | 0.79 | 0.94 | 31 | empty |
| 3 | 178 | 0.75 | 0.92 | 33 | empty |
| 4 | 493 | 0.71 | 0.81 | 44 | GDD |
| 5 | 548 | 0.71 | 0.80 | 51 | GDD |
Interfaces
20 interfaces between chains.
- C–D · 988 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 968 Ų buried · 7 hydrogen bonds · protein-protein
- K–D · 759 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 751 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 735 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7D72 · Cryo-EM structures of human GMPPA/GMPPB complex bound to GDP-Mannose · the same entry in another collection · chain L against L, 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 Q9Y5P6
- Every structure of UniProt Q96IJ6
- Elsewhere: RCSB PDB 7D72 · PDBe 7D72 · UniProt Q9Y5P6 · UniProt Q96IJ6
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