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Crystal structure of the gt domain of clostridium difficile toxin a (tcda) in complex with udp and manganese
Analyse Crystal structure of the gt domain of clostridium difficile toxin a (tcda) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DMW
- Type
- protein
- Length
- 535 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin a
- EC
- 2.4.1.-
- UniProt
- P16154
- Ligands
- UDP, MN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin a (EC 2.4.1.-) | protein | 535 | 58% helix, 8% strand | P16154 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.72 | 0.77 | 59 | MN, UDP |
| 2 | 189 | 0.48 | 0.76 | 32 | empty |
| 3 | 133 | 0.45 | 0.77 | 26 | empty |
| 4 | 101 | 0.40 | 0.76 | 19 | empty |
Compared structures
- 4DMW · Crystal structure of the GT domain of Clostridium difficile toxin A (TcdA) in complex… · 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 P16154
- Elsewhere: RCSB PDB 4DMW · PDBe 4DMW · UniProt P16154
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