Research workbench
Carboxyltransferase domain of a single-chain bacterial carboxylase
Analyse Carboxyltransferase domain of a single-chain bacterial carboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FIF
- Type
- protein
- Length
- 3,078 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxylase
- UniProt
- Q9RYK2
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxylase | protein | 507 | 38% helix, 18% strand | Q9RYK2 |
| B | Carboxylase | protein | 519 | 38% helix, 18% strand | Q9RYK2 |
| C | Carboxylase | protein | 507 | 39% helix, 18% strand | Q9RYK2 |
| D | Carboxylase | protein | 536 | 40% helix, 18% strand | Q9RYK2 |
| E | Carboxylase | protein | 503 | 40% helix, 18% strand | Q9RYK2 |
| F | Carboxylase | protein | 506 | 39% helix, 19% strand | Q9RYK2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, F, B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.86 | 0.87 | 128 | EDO |
| 2 | 971 | 0.86 | 0.87 | 121 | EDO |
| 3 | 947 | 0.86 | 0.87 | 124 | empty |
| 4 | 235 | 0.75 | 0.89 | 36 | empty |
| 5 | 199 | 0.74 | 0.90 | 35 | empty |
Interfaces
12 interfaces between chains.
- B–E · 3960 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 3932 Ų buried · 48 hydrogen bonds · protein-protein
- A–F · 3863 Ų buried · 46 hydrogen bonds · protein-protein
- C–F · 1543 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1499 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5FIF · Carboxyltransferase domain of a single-chain bacterial carboxylase · the same entry in another collection · chain B against B, 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 Q9RYK2
- Elsewhere: RCSB PDB 5FIF · PDBe 5FIF · UniProt Q9RYK2
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