Research workbench
The structure of N-formimino-L-glutamate iminohydrolase from pseudomonas aeruginosa complexed with N-formimino-L-aspartate
Analyse The structure of N-formimino-L-glutamate iminohydrolase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RDV
- Type
- protein
- Length
- 1,803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-formimino-L-glutamate iminohydrolase
- UniProt
- Q9HU77
- Ligands
- NFQ, ZN, PO4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-formimino-L-glutamate iminohydrolase | protein | 450 | 41% helix, 23% strand | Q9HU77 |
| B, C, D | N-formimino-L-glutamate iminohydrolase | protein | 451 | 41% helix, 23% strand | Q9HU77 |
Ligands and binding sites
- NFQ · N-[(E)-iminomethyl]-L-aspartic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains D
- GOL · Glycerol · additive · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.83 | 0.87 | 67 | empty |
| 2 | 879 | 0.81 | 0.83 | 69 | empty |
| 3 | 66 | 0.75 | 0.99 | 20 | NFQ |
| 4 | 64 | 0.73 | 0.98 | 20 | NFQ |
| 5 | 64 | 0.73 | 0.98 | 20 | NFQ |
Interfaces
5 interfaces between chains.
- C–D · 2821 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 2811 Ų buried · 68 hydrogen bonds · protein-protein
- B–D · 509 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 171 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 122 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4RDV · The structure of N-formimino-L-Glutamate Iminohydrolase from Pseudomonas aeruginosa… · the same entry in another collection · chain D against D, 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 Q9HU77
- Elsewhere: RCSB PDB 4RDV · PDBe 4RDV · UniProt Q9HU77
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