Research workbench
Crystal structure of E. COLI allantoinase with iron ions at the metal center
Analyse Crystal structure of E. COLI allantoinase with iron ions at the metal center in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E74
- Type
- protein
- Length
- 1,719 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allantoinase
- EC
- 3.5.2.5
- UniProt
- P77671
- Ligands
- FE
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Allantoinase (EC 3.5.2.5) | protein | 429 | 35% helix, 22% strand | P77671 |
| B | Allantoinase (EC 3.5.2.5) | protein | 433 | 35% helix, 23% strand | P77671 |
| C | Allantoinase (EC 3.5.2.5) | protein | 428 | 36% helix, 22% strand | P77671 |
Ligands and binding sites
- FE · Fe (III) 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
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.76 | 0.96 | 21 | empty |
| 2 | 72 | 0.72 | 0.96 | 18 | empty |
| 3 | 646 | 0.67 | 0.76 | 83 | FE |
| 4 | 414 | 0.64 | 0.78 | 56 | FE |
| 5 | 391 | 0.61 | 0.77 | 59 | FE |
Interfaces
4 interfaces between chains.
- B–C · 1032 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1010 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 822 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 789 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered, carboxylation).
Compared structures
- 3E74 · Crystal structure of E. coli allantoinase with iron ions at the metal center · the same entry in another collection · chain D against D, TM-score 1.00
- P77671 · AlphaFold monomer V2.0 prediction for allantoinase (P77671) · a predicted model of the same protein · chain C 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 P77671
- Elsewhere: RCSB PDB 3E74 · PDBe 3E74 · UniProt P77671
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