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The crystal structure of the first enzyme of pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase from mycobacterium tuberculosis shows a decameric assembly and terminal helix-swapping
Analyse The crystal structure of the first enzyme of pantothenate biosynthetic pathway… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OY0
- Type
- protein
- Length
- 1,240 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketopantoate hydroxymethyltransferase
- EC
- 2.1.2.11
- UniProt
- P0A5Q8
- Ligands
- MG
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Ketopantoate hydroxymethyltransferase (EC 2.1.2.11) | protein | 248 | 44% helix, 16% strand | P0A5Q8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.64 | 0.76 | 80 | MG |
| 2 | 526 | 0.64 | 0.76 | 69 | MG |
| 3 | 541 | 0.64 | 0.76 | 70 | MG |
| 4 | 407 | 0.60 | 0.76 | 54 | MG |
| 5 | 167 | 0.52 | 0.79 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–C · 383 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 379 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 377 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 362 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1OY0 · The crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway… · 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 P0A5Q8
- Elsewhere: RCSB PDB 1OY0 · PDBe 1OY0 · UniProt P0A5Q8
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