Research workbench
Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state I)
Analyse Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D73
- Type
- protein
- Length
- 4,495 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-1-phosphate guanyltransferase alpha; Mannose-1-phosphate guanyltransferase beta
- EC
- 2.7.7.13
- UniProt
- Q96IJ6, Q9Y5P6
- Ligands
- GTP, GDD
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 4 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 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, 28% strand | Q96IJ6 |
| E, G, I, J, K, L, H | Mannose-1-phosphate guanyltransferase beta (EC 2.7.7.13) | protein | 360 | 22% helix, 27% strand | Q9Y5P6 |
| F | Mannose-1-phosphate guanyltransferase beta (EC 2.7.7.13) | protein | 350 | 24% helix, 28% strand | Q9Y5P6 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 10 copies · chains B, E, D, F, G, I, J, K, L, H
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 2 copies · chains A, C
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 | 145 | 0.78 | 0.95 | 33 | empty |
| 2 | 165 | 0.76 | 0.93 | 32 | empty |
| 3 | 625 | 0.73 | 0.80 | 61 | GTP |
| 4 | 629 | 0.73 | 0.80 | 59 | GTP |
| 5 | 331 | 0.72 | 0.85 | 40 | GDD |
Interfaces
21 interfaces between chains.
- C–D · 987 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 987 Ų buried · 16 hydrogen bonds · protein-protein
- C–I · 727 Ų buried · 14 hydrogen bonds · protein-protein
- D–K · 713 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 710 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7D73 · Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (State I) · the same entry in another collection · chain H against H, 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 Q96IJ6
- Every structure of UniProt Q9Y5P6
- Elsewhere: RCSB PDB 7D73 · PDBe 7D73 · UniProt Q96IJ6 · UniProt Q9Y5P6
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