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Crystal structure of transketolase from chlamydomonas reinhardtii in complex with tpp and MG2+
Analyse Crystal structure of transketolase from chlamydomonas reinhardtii in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ND5
- Type
- protein
- Length
- 1,338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transketolase
- EC
- 2.2.1.1
- UniProt
- A8IAN1
- Ligands
- TPP, MG
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transketolase (EC 2.2.1.1) | protein | 669 | 45% helix, 13% strand | A8IAN1 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.75 | 0.87 | 51 | MG, TPP |
| 2 | 324 | 0.74 | 0.86 | 47 | MG, TPP |
| 3 | 356 | 0.60 | 0.77 | 40 | empty |
| 4 | 143 | 0.57 | 0.83 | 33 | empty |
| 5 | 158 | 0.53 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 4279 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 5ND5 · Crystal structure of transketolase from Chlamydomonas reinhardtii in complex with TPP and… · 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 A8IAN1
- Elsewhere: RCSB PDB 5ND5 · PDBe 5ND5 · UniProt A8IAN1
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