Research workbench
Structure of three-domain heme-cu nitrite reductase from ralstonia pickettii at 1.6 a resolution
Analyse Structure of three-domain heme-cu nitrite reductase from ralstonia pickettii at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AX3
- Type
- protein
- Length
- 1,823 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- E2STD2
- Ligands
- HEC, CU
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 456 | 21% helix, 34% strand | E2STD2 |
| B, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 455 | 20% helix, 34% strand | E2STD2 |
| D | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 457 | 20% helix, 33% strand | E2STD2 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.81 | 0.92 | 37 | empty |
| 2 | 555 | 0.77 | 0.84 | 67 | HEC |
| 3 | 507 | 0.76 | 0.84 | 63 | HEC |
| 4 | 223 | 0.76 | 0.90 | 36 | HEC |
| 5 | 537 | 0.75 | 0.82 | 69 | HEC |
Interfaces
5 interfaces between chains.
- C–D · 515 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 491 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 122 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 115 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 96 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 4AX3 · Structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.6 A… · the same entry in another collection · chain A 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 E2STD2
- Elsewhere: RCSB PDB 4AX3 · PDBe 4AX3 · UniProt E2STD2
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