Research workbench
Crystal structure of PTMU3 complexed with ptm substrate
Analyse Crystal structure of PTMU3 complexed with ptm substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OMQ
- Type
- protein
- Length
- 712 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PTMU3
- UniProt
- A0A0A0UVH9
- Ligands
- MZD, MN
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PTMU3 | protein | 356 | 44% helix, 17% strand | A0A0A0UVH9 |
Ligands and binding sites
- MZD · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] (5beta,7alpha, 8alpha,10alpha,11alpha,13alpha)-7-hydroxy-11,16-epoxykaurane-18-thioate · ligand · chains A, B
- MN · Manganese (II) ion · metal · 7 copies · chains A, B
- ACT · Acetate ion · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.83 | 0.89 | 50 | MZD |
| 2 | 906 | 0.80 | 0.82 | 57 | MN |
| 3 | 124 | 0.39 | 0.74 | 27 | empty |
| 4 | 78 | 0.38 | 0.78 | 20 | empty |
| 5 | 80 | 0.38 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2607 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6OMQ · Crystal structure of PtmU3 complexed with PTM substrate · 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 A0A0A0UVH9
- Elsewhere: RCSB PDB 6OMQ · PDBe 6OMQ · UniProt A0A0A0UVH9
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