Research workbench
Crystal structure of aibc
Analyse Crystal structure of aibc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K1S
- Type
- protein
- Length
- 1,382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, zinc-binding dehydrogenase family
- UniProt
- Q1D4I2
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Oxidoreductase, zinc-binding dehydrogenase family | protein | 358 | 30% helix, 28% strand | Q1D4I2 |
| B | Oxidoreductase, zinc-binding dehydrogenase family | protein | 333 | 28% helix, 28% strand | Q1D4I2 |
| D | Oxidoreductase, zinc-binding dehydrogenase family | protein | 333 | 31% helix, 30% strand | Q1D4I2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.77 | 0.79 | 103 | ZN |
| 2 | 602 | 0.75 | 0.82 | 67 | empty |
| 3 | 787 | 0.72 | 0.77 | 68 | empty |
| 4 | 736 | 0.71 | 0.77 | 60 | empty |
| 5 | 431 | 0.59 | 0.75 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1472 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1408 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 477 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 66 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 61 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5K1S · crystal structure of AibC · 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 Q1D4I2
- Elsewhere: RCSB PDB 5K1S · PDBe 5K1S · UniProt Q1D4I2
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