MolNFT v1 · #104578 · protein
Crystal structure of 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase from bacillus anthracis
4QEZ: “Crystal structure of 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase from bacillus anthracis”. X-ray diffraction, 1 ligand (ADE), 5 pockets (best druggability 0.76). MolNFT v1 #104578 on GenesisL1: 3D structure, binding…
- PDB
- 4QEZ
- Type
- protein
- Length
- 685 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase
- EC
- 3.2.2.9
- UniProt
- Q81LL4
- Ligands
- ADE
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 231 | 35% helix, 31% strand | Q81LL4 |
| A | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 223 | 36% helix, 33% strand | Q81LL4 |
Ligands and binding sites
- ADE · Adenine · ligand · 3 copies · chains B, A, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.76 | 0.99 | 22 | ADE, TRS |
| 2 | 179 | 0.65 | 0.85 | 35 | ADE, TRS |
| 3 | 598 | 0.64 | 0.75 | 57 | empty |
| 4 | 64 | 0.61 | 0.91 | 20 | TRS, ADE |
| 5 | 151 | 0.44 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1546 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QEZ · Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from… · the same entry in another collection · chain B against B, TM-score 1.00
- Q81LL4 · AlphaFold monomer V2.0 prediction for 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine… · a predicted model of the same protein · chain A 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 Q81LL4
- Elsewhere: RCSB PDB 4QEZ · PDBe 4QEZ · UniProt Q81LL4
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