Research workbench
Crystal structure of HMTH1 N33A in complex with LW14 in the presence of acetate
Analyse Crystal structure of HMTH1 N33A in complex with LW14 in the presence of acetate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GLL
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydro-8-oxoguanine triphosphatase
- EC
- 3.6.1.55, 3.6.1.56
- UniProt
- P36639
- Ligands
- BU8, SO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 158 | 16% helix, 49% strand | P36639 |
| B | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 157 | 16% helix, 43% strand | P36639 |
Ligands and binding sites
- BU8 · 1~{H}-imidazo[4,5-b]pyridin-2-amine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.78 | 0.82 | 70 | SO4 |
| 2 | 247 | 0.72 | 0.86 | 31 | BU8, ACT |
| 3 | 278 | 0.68 | 0.83 | 31 | BU8, ACT |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6GLL · Crystal structure of hMTH1 N33A in complex with LW14 in the presence of acetate · the same entry in another collection · chain A against A, TM-score 1.00
- P36639 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-8-oxoguanine triphosphatase (P36639) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P36639
- Elsewhere: RCSB PDB 6GLL · PDBe 6GLL · UniProt P36639
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