Research workbench
Formate bound to oxidized wild type afnir
Analyse Formate bound to oxidized wild type afnir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PP8
- Type
- protein
- Length
- 1,008 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
- CU1, CU
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 336 | 11% helix, 43% strand | P38501 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 3 copies · chains A, B, C
- CU · Copper (II) ion · metal · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 8 copies · chains A, B, C
- FMT · Formic acid · additive · 3 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.84 | 0.96 | 31 | TRS |
| 2 | 531 | 0.80 | 0.87 | 63 | ACT |
| 3 | 61 | 0.72 | 0.98 | 18 | empty |
| 4 | 60 | 0.71 | 0.97 | 18 | empty |
| 5 | 111 | 0.49 | 0.80 | 37 | CU, ACT, FMT |
Interfaces
3 interfaces between chains.
- A–B · 2107 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2103 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2091 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2PP8 · Formate bound to oxidized wild type AfNiR · 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 P38501
- Elsewhere: RCSB PDB 2PP8 · PDBe 2PP8 · UniProt P38501
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