MolNFT v1 · #121784 · protein
Shewanella denitrificans nitrous oxide reductase, CA2+-reconstituted form
5I5M · Nitrous-oxide reductase: “Shewanella denitrificans nitrous oxide reductase, CA2+-reconstituted form”. X-ray diffraction, 2 ligands (CA, SO4), 9 pockets (best druggability 0.81). MolNFT v1 #121784 on GenesisL1: 3D structure, binding…
- PDB
- 5I5M
- Type
- protein
- Length
- 1,151 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrous-oxide reductase
- EC
- 1.7.2.4
- UniProt
- Q12M27
- Ligands
- CA, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 575 | 11% helix, 42% strand | Q12M27 |
| B | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 576 | 11% helix, 41% strand | Q12M27 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- BU3 · (R,R)-2,3-butanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.81 | 0.99 | 20 | empty |
| 2 | 381 | 0.80 | 0.89 | 46 | empty |
| 3 | 115 | 0.80 | 0.98 | 18 | empty |
| 4 | 56 | 0.73 | 0.99 | 19 | empty |
| 5 | 180 | 0.51 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 5910 Ų buried · 89 hydrogen bonds · protein-protein
Compared structures
- 5I5M · Shewanella denitrificans nitrous oxide reductase, Ca2+-reconstituted form · 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 Q12M27
- Elsewhere: RCSB PDB 5I5M · PDBe 5I5M · UniProt Q12M27
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