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Crystal structure of N5-carboxyaminoimidazole ribonucleotide mutase (pure) from legionella pneumophila
Analyse Crystal structure of N5-carboxyaminoimidazole ribonucleotide mutase (pure) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O55
- Type
- protein
- Length
- 646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N5-carboxyaminoimidazole ribonucleotide mutase
- EC
- 5.4.99.18
- UniProt
- Q5ZYZ3
- Ligands
- CL
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | N5-carboxyaminoimidazole ribonucleotide mutase (EC 5.4.99.18) | protein | 161 | 49% helix, 17% strand | Q5ZYZ3 |
| D | N5-carboxyaminoimidazole ribonucleotide mutase (EC 5.4.99.18) | protein | 163 | 48% helix, 15% strand | Q5ZYZ3 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, B, C
- PG4 · Tetraethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.57 | 0.74 | 47 | empty |
| 2 | 377 | 0.55 | 0.74 | 43 | empty |
| 3 | 328 | 0.54 | 0.74 | 42 | empty |
| 4 | 259 | 0.50 | 0.74 | 33 | empty |
| 5 | 145 | 0.42 | 0.74 | 17 | EDO, PG4 |
Interfaces
4 interfaces between chains.
- C–D · 676 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 668 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 650 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 646 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6O55 · Crystal Structure of N5-carboxyaminoimidazole ribonucleotide mutase (PurE) from… · 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 Q5ZYZ3
- Elsewhere: RCSB PDB 6O55 · PDBe 6O55 · UniProt Q5ZYZ3
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