MolNFT v1 · #127549 · protein
Crystal structure of the decarboxylase AIBA/AIBB in complex with a possible transition state analog
5MZY · Glutaconate CoA-transferase family, subunit a: “Crystal structure of the decarboxylase AIBA/AIBB in complex with a possible transition state analog”. X-ray diffraction, 1 ligand (8EZ), 9 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5MZY
- Type
- protein
- Length
- 1,010 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaconate CoA-transferase family, subunit a; Glutaconate CoA-transferase family…
- UniProt
- Q1D4I4, Q1D4I3
- Ligands
- 8EZ
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaconate CoA-transferase family, subunit a | protein | 262 | 31% helix, 26% strand | Q1D4I4 |
| C | Glutaconate CoA-transferase family, subunit a | protein | 263 | 32% helix, 27% strand | Q1D4I4 |
| D | Glutaconate CoA-transferase family, subunit B | protein | 241 | 27% helix, 27% strand | Q1D4I3 |
| B | Glutaconate CoA-transferase family, subunit B | protein | 244 | 26% helix, 25% strand | Q1D4I3 |
Ligands and binding sites
- 8EZ · (1~{R},2~{S})-2-methylcyclohexane-1-carboxylic acid · ligand · 2 copies · chains C, D, A, B
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.83 | 0.84 | 60 | empty |
| 2 | 611 | 0.78 | 0.83 | 63 | 8EZ |
| 3 | 530 | 0.75 | 0.82 | 53 | 8EZ, GOL |
| 4 | 120 | 0.41 | 0.75 | 16 | empty |
| 5 | 89 | 0.39 | 0.77 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1832 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1813 Ų buried · 27 hydrogen bonds · protein-protein
- C–B · 882 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 847 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 829 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MZY · Crystal structure of the decarboxylase AibA/AibB in complex with a possible transition… · 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 Q1D4I4
- Every structure of UniProt Q1D4I3
- Elsewhere: RCSB PDB 5MZY · PDBe 5MZY · UniProt Q1D4I4 · UniProt Q1D4I3
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