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Crystal structure of possible 2-hydroxychromene-2-carboxylate isomerase from rhodobacter sphaeroides
Analyse Crystal structure of possible 2-hydroxychromene-2-carboxylate isomerase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FZ5
- Type
- protein
- Length
- 754 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Possible 2-hydroxychromene-2-carboxylate isomerase
- UniProt
- Q3J568
- Ligands
- GSH, CA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Possible 2-hydroxychromene-2-carboxylate isomerase | protein | 190 | 56% helix, 9% strand | Q3J568 |
| B, D | Possible 2-hydroxychromene-2-carboxylate isomerase | protein | 186 | 56% helix, 11% strand | Q3J568 |
| C | Possible 2-hydroxychromene-2-carboxylate isomerase | protein | 192 | 58% helix, 10% strand | Q3J568 |
Ligands and binding sites
- GSH · Glutathione · ligand · 3 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · chains D
- PGE · Triethylene glycol · additive · chains B, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.80 | 0.81 | 110 | GSH, PGE |
| 2 | 653 | 0.69 | 0.77 | 50 | GSH |
| 3 | 275 | 0.57 | 0.77 | 30 | empty |
| 4 | 261 | 0.53 | 0.75 | 31 | empty |
| 5 | 50 | 0.29 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1236 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1213 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 458 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3FZ5 · Crystal structure of possible 2-hydroxychromene-2-carboxylate isomerase from Rhodobacter… · 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 Q3J568
- Elsewhere: RCSB PDB 3FZ5 · PDBe 3FZ5 · UniProt Q3J568
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