Research workbench
Crystal structure of methanobrevibacter smithii DPH2 bound to 5'- methylthioadenosine
Analyse Crystal structure of methanobrevibacter smithii DPH2 bound to 5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q2E
- Type
- protein
- Length
- 659 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase
- EC
- 2.5.1.108
- UniProt
- A5UMY5
- Ligands
- MTA, SF4, CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase (EC 2.5.1.108) | protein | 330 | 39% helix, 20% strand | A5UMY5 |
| B | 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase (EC 2.5.1.108) | protein | 329 | 39% helix, 19% strand | A5UMY5 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.72 | 0.83 | 46 | MTA, SF4 |
| 2 | 552 | 0.71 | 0.80 | 76 | MTA, SF4 |
| 3 | 224 | 0.69 | 0.86 | 38 | empty |
| 4 | 110 | 0.39 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1735 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6Q2E · Crystal structure of Methanobrevibacter smithii Dph2 bound to 5'-methylthioadenosine · 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 A5UMY5
- Elsewhere: RCSB PDB 6Q2E · PDBe 6Q2E · UniProt A5UMY5
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