MolNFT v1 · #162850 · protein
Recombinant pseudomonas stutzeri nitrous oxide reductase, form I
6RL0 · Nitrous-oxide reductase: “Recombinant pseudomonas stutzeri nitrous oxide reductase, form I”. X-ray diffraction, 6 ligands (CUK, CUA, CA), 13 pockets (best druggability 0.80). MolNFT v1 #162850 on GenesisL1: 3D structure, binding…
- PDB
- 6RL0
- Type
- protein
- Length
- 2,331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrous-oxide reductase
- EC
- 1.7.2.4
- UniProt
- P19573
- Ligands
- CUK, CUA, CA, K, NA, CL
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 584 | 11% helix, 41% strand | P19573 |
| C | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 582 | 11% helix, 42% strand | P19573 |
| D | Nitrous-oxide reductase (EC 1.7.2.4) | protein | 581 | 12% helix, 42% strand | P19573 |
Ligands and binding sites
- CUK · [4Cu:2S] cluster · ligand · 4 copies · chains A, D, B, C
- CUA · Dinuclear copper ion · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, D, B, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 5 copies · chains A, B, C, D
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.80 | 0.92 | 37 | empty |
| 2 | 259 | 0.80 | 0.92 | 41 | empty |
| 3 | 265 | 0.51 | 0.75 | 39 | empty |
| 4 | 213 | 0.49 | 0.75 | 30 | empty |
| 5 | 197 | 0.47 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5841 Ų buried · 74 hydrogen bonds · protein-protein
- A–D · 5714 Ų buried · 77 hydrogen bonds · protein-protein
- B–D · 276 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 P19573
- Elsewhere: RCSB PDB 6RL0 · PDBe 6RL0 · UniProt P19573
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