MolNFT v1 · #161058 · protein
Crystal structure of methanobrevibacter smithii DPH2 in complex with methanobrevibacter smithii elongation factor 2
6Q2D · 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase: “Crystal structure of methanobrevibacter smithii DPH2 in complex with methanobrevibacter smithii elongation…”. X-ray diffraction, 1 ligand (SF4), 20 pockets (best druggability 0.88).…
- PDB
- 6Q2D
- Type
- protein
- Length
- 1,680 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase; Elongation factor 2
- EC
- 2.5.1.108
- UniProt
- A5UMY5, A0A2H4U7K7
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase (EC 2.5.1.108) | protein | 329 | 39% helix, 21% strand | A5UMY5 |
| B | 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase (EC 2.5.1.108) | protein | 325 | 40% helix, 21% strand | A5UMY5 |
| C | Elongation factor 2 | protein | 700 | 36% helix, 28% strand | A0A2H4U7K7 |
| F | Elongation factor 2 | protein | 326 | 33% helix, 32% strand | A0A2H4U7K7 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.88 | 0.89 | 146 | SF4 |
| 2 | 404 | 0.82 | 0.91 | 65 | SF4 |
| 3 | 950 | 0.79 | 0.81 | 82 | empty |
| 4 | 309 | 0.70 | 0.84 | 45 | empty |
| 5 | 219 | 0.68 | 0.86 | 39 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1780 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1081 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 844 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 558 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 540 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Q2D · Crystal structure of Methanobrevibacter smithii Dph2 in complex with Methanobrevibacter… · 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
- Every structure of UniProt A0A2H4U7K7
- Elsewhere: RCSB PDB 6Q2D · PDBe 6Q2D · UniProt A5UMY5 · UniProt A0A2H4U7K7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.