Research workbench
Crystal structure of MET150GLY afnir with methylsulfanyl methane bound
Analyse Crystal structure of MET150GLY afnir with methylsulfanyl methane bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZDQ
- Type
- protein
- Length
- 1,007 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- P38501
- Ligands
- MSM, CU
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 335 | 12% helix, 43% strand | P38501 |
| B, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 336 | 12% helix, 43% strand | P38501 |
Ligands and binding sites
- MSM · (methylsulfanyl)methane · ligand · 3 copies · chains A, B, C
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.84 | 0.96 | 31 | empty |
| 2 | 555 | 0.81 | 0.87 | 60 | empty |
| 3 | 82 | 0.75 | 0.97 | 23 | MSM |
| 4 | 87 | 0.73 | 0.96 | 24 | MSM |
| 5 | 56 | 0.71 | 0.98 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2121 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 2117 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2097 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 1ZDQ · Crystal Structure of Met150Gly AfNiR with Methylsulfanyl Methane Bound · the same entry in another collection · chain A against A, TM-score 1.00
- P38501 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (P38501) · a predicted model of the same protein · chain B 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 P38501
- Elsewhere: RCSB PDB 1ZDQ · PDBe 1ZDQ · UniProt P38501
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