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Crystal structure of ternary complex of E.COLI HPPK(W89A) with mgampcpp and 6-hydroxymethylpterin
Analyse Crystal structure of ternary complex of E.COLI HPPK(W89A) with mgampcpp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TMM
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
- EC
- 2.7.6.3
- UniProt
- P26281
- Ligands
- APC, HHR, MG, CL
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 158 | 30% helix, 27% strand | P26281 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- HHR · 6-hydroxymethylpterin · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.61 | 0.78 | 43 | MG, APC, HHR |
| 2 | 289 | 0.60 | 0.78 | 39 | MG, APC, HHR |
| 3 | 51 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1TMM · Crystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and… · the same entry in another collection · chain A against A, TM-score 1.00
- P26281 · AlphaFold monomer V2.0 prediction for 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P26281
- Elsewhere: RCSB PDB 1TMM · PDBe 1TMM · UniProt P26281
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