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Crystal structure of clda, the first cyclomaltodextrin glucanotransferase with a three-domain ABC distribution
Analyse Crystal structure of clda, the first cyclomaltodextrin glucanotransferase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WNI
- Type
- protein
- Length
- 987 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclomaltodextrin glucanotransferase
- EC
- 2.4.1.19
- UniProt
- U5CJP3
- Ligands
- CA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclomaltodextrin glucanotransferase (EC 2.4.1.19) | protein | 494 | 31% helix, 24% strand | U5CJP3 |
| B | Cyclomaltodextrin glucanotransferase (EC 2.4.1.19) | protein | 493 | 31% helix, 24% strand | U5CJP3 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 17 copies · chains A, B
- FLC · Citrate anion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.72 | 0.76 | 106 | PEG, FLC |
| 2 | 432 | 0.65 | 0.78 | 51 | FLC, PEG |
| 3 | 307 | 0.61 | 0.78 | 35 | FLC |
| 4 | 98 | 0.39 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 306 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WNI · Crystal structure of CldA, the first cyclomaltodextrin glucanotransferase with a… · 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 U5CJP3
- Elsewhere: RCSB PDB 6WNI · PDBe 6WNI · UniProt U5CJP3
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