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Crystal structure of thiamin pyrophosphokinase family protein from enterococcus faecalis, northeast structural genomics consortium target EFR150
Analyse Crystal structure of thiamin pyrophosphokinase family protein from enterococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MEL
- Type
- protein
- Length
- 853 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamin pyrophosphokinase family protein
- UniProt
- Q82ZE3
- Ligands
- TPP, MG, PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Thiamin pyrophosphokinase family protein | protein | 213 | 23% helix, 35% strand | Q82ZE3 |
| C | Thiamin pyrophosphokinase family protein | protein | 214 | 24% helix, 37% strand | Q82ZE3 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 11 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.78 | 0.81 | 83 | TPP, MG |
| 2 | 898 | 0.77 | 0.80 | 77 | TPP, MG |
| 3 | 754 | 0.73 | 0.79 | 57 | PO4, MG |
| 4 | 662 | 0.72 | 0.79 | 57 | PO4, MG |
| 5 | 165 | 0.49 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1555 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1508 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 625 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3MEL · Crystal Structure of Thiamin pyrophosphokinase family protein from Enterococcus faecalis… · 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 Q82ZE3
- Elsewhere: RCSB PDB 3MEL · PDBe 3MEL · UniProt Q82ZE3
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