Research workbench
Cobt from methanocaldococcus jannaschii in complex with alpha-ribozole 5'-phosphate, nicotinic acid, and nicotinic acid mononucleotide
Analyse Cobt from methanocaldococcus jannaschii in complex with alpha-ribozole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PU6
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0284 protein MJ1598
- UniProt
- Q58993
- Ligands
- NCN, RBZ, NIO
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0284 protein MJ1598 | protein | 344 | 47% helix, 13% strand | Q58993 |
| B | UPF0284 protein MJ1598 | protein | 343 | 46% helix, 12% strand | Q58993 |
Ligands and binding sites
- NCN · Nicotinate mononucleotide · ligand · chains A
- RBZ · Alpha-ribazole-5'-phosphate · ligand · chains B
- NIO · Nicotinic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.78 | 0.90 | 40 | NCN |
| 2 | 225 | 0.73 | 0.88 | 41 | RBZ, NIO |
| 3 | 101 | 0.56 | 0.85 | 22 | empty |
| 4 | 163 | 0.43 | 0.74 | 24 | empty |
| 5 | 60 | 0.31 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 964 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6PU6 · CobT from Methanocaldococcus jannaschii in complex with Alpha-Ribozole 5'-Phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58993 · AlphaFold monomer V2.0 prediction for UPF0284 protein MJ1598 (Q58993) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q58993
- Elsewhere: RCSB PDB 6PU6 · PDBe 6PU6 · UniProt Q58993
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