Research workbench
Crystal structure of unda complexed with iron nitrilotriacetate
Analyse Crystal structure of unda complexed with iron nitrilotriacetate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UFK
- Type
- protein
- Length
- 800 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unda
- UniProt
- F8UWD6
- Ligands
- HEC, NTA, FE, MG, CA, O
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unda | protein | 800 | 23% helix, 23% strand | F8UWD6 |
Ligands and binding sites
- HEC · Heme C · ligand · 11 copies · chains A
- NTA · Nitrilotriacetic acid · ligand · 4 copies · chains A
- FE · Fe (III) ion · metal · 4 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- O · Oxygen atom · ion · 2 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.87 | 0.88 | 103 | HEC |
| 2 | 1137 | 0.87 | 0.88 | 140 | HEC |
| 3 | 456 | 0.75 | 0.84 | 46 | empty |
| 4 | 193 | 0.43 | 0.73 | 34 | empty |
| 5 | 100 | 0.42 | 0.78 | 26 | empty |
Modifications
Observed in the structure: 22 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 3UFK · Crystal structure of UndA complexed with Iron Nitrilotriacetate · 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 F8UWD6
- Elsewhere: RCSB PDB 3UFK · PDBe 3UFK · UniProt F8UWD6
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