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Structure of the archaeal GTP:ADOCBI-P guanylyltransferase (coby) from methanocaldococcus jannaschii
Analyse Structure of the archaeal GTP:ADOCBI-P guanylyltransferase (coby) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RSB
- Type
- protein
- Length
- 723 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylcobinamide-phosphate guanylyltransferase
- EC
- 2.7.7.62
- UniProt
- Q58517
- Ligands
- GTP
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylcobinamide-phosphate guanylyltransferase (EC 2.7.7.62) | protein | 177 | 29% helix, 27% strand | Q58517 |
| B | Adenosylcobinamide-phosphate guanylyltransferase (EC 2.7.7.62) | protein | 185 | 30% helix, 28% strand | Q58517 |
| C | Adenosylcobinamide-phosphate guanylyltransferase (EC 2.7.7.62) | protein | 181 | 30% helix, 24% strand | Q58517 |
| D | Adenosylcobinamide-phosphate guanylyltransferase (EC 2.7.7.62) | protein | 180 | 31% helix, 27% strand | Q58517 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.70 | 0.75 | 115 | GTP |
| 2 | 198 | 0.67 | 0.86 | 28 | empty |
| 3 | 374 | 0.63 | 0.78 | 30 | empty |
| 4 | 436 | 0.60 | 0.75 | 44 | empty |
| 5 | 257 | 0.52 | 0.75 | 48 | GTP |
Interfaces
4 interfaces between chains.
- A–C · 547 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 454 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 426 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 43 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 3RSB · Structure of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q58517 · AlphaFold monomer V2.0 prediction for adenosylcobinamide-phosphate guanylyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q58517
- Elsewhere: RCSB PDB 3RSB · PDBe 3RSB · UniProt Q58517
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