Research workbench
Crystal structure of cobt from methanocaldococcus jannaschii in complex with adenine alpha-ribotide and nicotinic acid
Analyse Crystal structure of cobt from methanocaldococcus jannaschii in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PT8
- Type
- protein
- Length
- 699 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0284 protein MJ1598
- UniProt
- Q58993
- Ligands
- AAM, NIO, PO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0284 protein MJ1598 | protein | 350 | 47% helix, 14% strand | Q58993 |
| B | UPF0284 protein MJ1598 | protein | 349 | 46% helix, 14% strand | Q58993 |
Ligands and binding sites
- AAM · Alpha-adenosine monophosphate · ligand · 2 copies · chains A, B
- NIO · Nicotinic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.81 | 0.98 | 34 | NIO, AAM |
| 2 | 140 | 0.81 | 0.98 | 33 | AAM, NIO |
| 3 | 142 | 0.38 | 0.72 | 26 | empty |
| 4 | 54 | 0.32 | 0.76 | 10 | empty |
| 5 | 65 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 997 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6PT8 · Crystal Structure of CobT from Methanocaldococcus jannaschii in complex with Adenine… · 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 6PT8 · PDBe 6PT8 · UniProt Q58993
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