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Crystal structure of a novel cyclase (PFAM04199).
Analyse Crystal structure of a novel cyclase (PFAM04199). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IBZ
- Type
- protein
- Length
- 1,215 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A0A0G3FEK2
- Ligands
- UVW
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 306 | 30% helix, 23% strand | A0A0G3FEK2 |
| B | Uncharacterized protein | protein | 308 | 28% helix, 23% strand | A0A0G3FEK2 |
| C | Uncharacterized protein | protein | 301 | 31% helix, 24% strand | A0A0G3FEK2 |
| D | Uncharacterized protein | protein | 300 | 31% helix, 23% strand | A0A0G3FEK2 |
Ligands and binding sites
- UVW · Acetylphosphate · ligand · 4 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.80 | 0.82 | 73 | UVW |
| 2 | 573 | 0.76 | 0.83 | 34 | empty |
| 3 | 238 | 0.68 | 0.84 | 42 | UVW |
| 4 | 261 | 0.67 | 0.83 | 39 | UVW |
| 5 | 382 | 0.64 | 0.79 | 45 | UVW |
Interfaces
6 interfaces between chains.
- B–D · 3501 Ų buried · 69 hydrogen bonds · protein-protein
- A–C · 3441 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 1111 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1106 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 457 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5IBZ · Crystal structure of a novel cyclase (pfam04199). · 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 A0A0G3FEK2
- Elsewhere: RCSB PDB 5IBZ · PDBe 5IBZ · UniProt A0A0G3FEK2
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