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Structure of the adenylation domain of an NAD+ dependent ligase
Analyse Structure of the adenylation domain of an NAD+ dependent ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B04
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (DNA ligase)
- EC
- 6.5.1.2
- UniProt
- O87703
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (DNA ligase) (EC 6.5.1.2) | protein | 310 | 41% helix, 20% strand | O87703 |
| B | Protein (DNA ligase) (EC 6.5.1.2) | protein | 311 | 42% helix, 22% strand | O87703 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.83 | 0.84 | 97 | empty |
| 2 | 549 | 0.75 | 0.83 | 49 | empty |
| 3 | 240 | 0.56 | 0.78 | 24 | empty |
| 4 | 108 | 0.56 | 0.84 | 23 | empty |
| 5 | 177 | 0.53 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 815 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
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 O87703
- Elsewhere: RCSB PDB 1B04 · PDBe 1B04 · UniProt O87703
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