Research workbench
Crystal structure of escherichia COLI L-arabinose isomerase (ecai) complexed with ribitol
Analyse Crystal structure of escherichia COLI L-arabinose isomerase (ecai) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F2D
- Type
- protein
- Length
- 1,494 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arabinose isomerase
- EC
- 5.3.1.4
- UniProt
- P08202
- Ligands
- RB0, MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L-arabinose isomerase (EC 5.3.1.4) | protein | 498 | 40% helix, 21% strand | P08202 |
Ligands and binding sites
- RB0 · D-ribitol · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- ACY · Acetic acid · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.81 | 0.87 | 63 | empty |
| 2 | 709 | 0.81 | 0.85 | 66 | empty |
| 3 | 550 | 0.81 | 0.87 | 58 | empty |
| 4 | 72 | 0.73 | 0.97 | 25 | empty |
| 5 | 241 | 0.73 | 0.88 | 31 | RB0 |
Interfaces
3 interfaces between chains.
- A–B · 2387 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2364 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 2163 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 modified (engineered).
Compared structures
- 4F2D · Crystal Structure of Escherichia coli L-arabinose Isomerase (ECAI) complexed with Ribitol · the same entry in another collection · chain A against A, TM-score 1.00
- P08202 · AlphaFold monomer V2.0 prediction for L-arabinose isomerase (P08202) · a predicted model of the same protein · 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 P08202
- Elsewhere: RCSB PDB 4F2D · PDBe 4F2D · UniProt P08202
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