MolNFT v1 · #151157 · protein
Crystal structure of the adenylate kinase from methanothermococcus thermolithotrophicus co-crystallized with tb-XO4
6HF7: “Crystal structure of the adenylate kinase from methanothermococcus thermolithotrophicus co-crystallized with…”. X-ray diffraction, 3 ligands (7MT, TB, MG), 7 pockets (best druggability 0.63). MolNFT v1 #151157 on GenesisL1: 3D…
- PDB
- 6HF7
- Type
- protein
- Length
- 573 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P43410
- Ligands
- 7MT, TB, MG
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Adenylate kinase (EC 2.7.4.3) | protein | 191 | 50% helix, 17% strand | P43410 |
Ligands and binding sites
- 7MT · Tb-Xo4 · ligand · 2 copies · chains A, B
- TB · Terbium(iii) ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.63 | 0.75 | 42 | empty |
| 2 | 393 | 0.58 | 0.75 | 39 | empty |
| 3 | 369 | 0.57 | 0.75 | 37 | empty |
| 4 | 69 | 0.53 | 0.86 | 13 | empty |
| 5 | 113 | 0.37 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 769 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 766 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6HF7 · Crystal structure of the adenylate kinase from Methanothermococcus thermolithotrophicus… · the same entry in another collection · chain A against A, TM-score 1.00
- P43410 · AlphaFold monomer V2.0 prediction for adenylate kinase (P43410) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P43410
- Elsewhere: RCSB PDB 6HF7 · PDBe 6HF7 · UniProt P43410
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