Research workbench
Crystal structure of CALS8 from micromonospora echinospora cocrystallized with NAD and tdp-glucose
Analyse Crystal structure of CALS8 from micromonospora echinospora cocrystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XR9
- Type
- protein
- Length
- 909 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALS8
- UniProt
- Q8KNF6
- Ligands
- NAD, TMP, NA
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALS8 | protein | 456 | 46% helix, 14% strand | Q8KNF6 |
| B | CALS8 | protein | 453 | 44% helix, 14% strand | Q8KNF6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- TMP · Thymidine-5'-phosphate · ligand · chains A, B
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.78 | 0.80 | 84 | empty |
| 2 | 970 | 0.78 | 0.80 | 85 | NAD, TMP |
| 3 | 77 | 0.42 | 0.80 | 17 | empty |
| 4 | 99 | 0.36 | 0.75 | 32 | empty |
| 5 | 79 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2773 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4XR9 · Crystal structure of CalS8 from Micromonospora echinospora cocrystallized with NAD and… · the same entry in another collection · chain A against A, 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 Q8KNF6
- Elsewhere: RCSB PDB 4XR9 · PDBe 4XR9 · UniProt Q8KNF6
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