Research workbench
Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state II)
Analyse Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D74
- Type
- protein
- Length
- 4,503 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
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B, C | Mannose-1-phosphate guanyltransferase alpha | protein | 406 | 22% helix, 29% strand | Q96IJ6 |
| E, F, H, I, J, K, L | Mannose-1-phosphate guanyltransferase beta (EC 2.7.7.13) | protein | 360 | 25% helix, 26% strand | Q9Y5P6 |
| G | Mannose-1-phosphate guanyltransferase beta (EC 2.7.7.13) | protein | 359 | 25% helix, 26% strand | Q9Y5P6 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 12 copies · chains A, D, B, C, E, F, G, H, I, J, K, L
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 | 1037 | 0.77 | 0.79 | 109 | GTP |
| 2 | 139 | 0.76 | 0.94 | 30 | empty |
| 3 | 142 | 0.75 | 0.94 | 30 | empty |
| 4 | 136 | 0.75 | 0.94 | 30 | empty |
| 5 | 144 | 0.75 | 0.93 | 28 | empty |
Interfaces
24 interfaces between chains.
- D–C · 1226 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1215 Ų buried · 18 hydrogen bonds · protein-protein
- C–I · 714 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 711 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 710 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7D74 · Cryo-EM structure of GMPPA/GMPPB complex bound to GTP (state II) · 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 Q96IJ6
- Every structure of UniProt Q9Y5P6
- Elsewhere: RCSB PDB 7D74 · PDBe 7D74 · UniProt Q96IJ6 · UniProt Q9Y5P6
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