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2.1 ångström resolution crystal structure of 5'-METHYLTHIOADENOSINE/S- adenosylhomocysteine nucleosidase (mtnn) from haemophilus influenzae pittii.
Analyse 2.1 ångström resolution crystal structure of 5'-METHYLTHIOADENOSINE/S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PO4
- Type
- protein
- Length
- 1,394 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase
- EC
- 3.2.2.9
- UniProt
- A0A0E1SMD9
- Ligands
- HCS, ADE, BO3
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 233 | 38% helix, 31% strand | A0A0E1SMD9 |
| B, D, E, F | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 232 | 37% helix, 31% strand | A0A0E1SMD9 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · 6 copies · chains A, B, C, D, E, F
- ADE · Adenine · ligand · 6 copies · chains A, B, C, D, E, F
- BO3 · Boric acid · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.77 | 0.83 | 74 | HCS, ADE, BO3 |
| 2 | 547 | 0.77 | 0.84 | 76 | HCS, ADE, BO3 |
| 3 | 102 | 0.72 | 0.93 | 23 | ADE, HCS, BO3 |
| 4 | 110 | 0.70 | 0.92 | 23 | ADE, BO3, HCS |
| 5 | 107 | 0.69 | 0.91 | 23 | HCS, ADE, BO3 |
Interfaces
7 interfaces between chains.
- A–B · 1469 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1463 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1463 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 489 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 488 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6PO4 · 2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine… · the same entry in another collection · chain B against B, 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 A0A0E1SMD9
- Elsewhere: RCSB PDB 6PO4 · PDBe 6PO4 · UniProt A0A0E1SMD9
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