Research workbench
Computational design of a high-affinity metalloprotein homotrimer containing a metal chelating non-canonical amino acid
Analyse Computational design of a high-affinity metalloprotein homotrimer containing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EIL
- Type
- protein
- Length
- 473 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tri-05
- Ligands
- BP5, FE
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tri-05 | protein | 157 | 50% helix, 0% strand | — |
| B, C | Tri-05 | protein | 158 | 49% helix, 0% strand | — |
Ligands and binding sites
- BP5 · 3-(2,2'-bipyridin-5-yl)-L-alanine · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.77 | 0.85 | 27 | BP5, FE |
| 2 | 54 | 0.36 | 0.79 | 14 | empty |
| 3 | 56 | 0.36 | 0.79 | 13 | empty |
| 4 | 73 | 0.34 | 0.76 | 19 | empty |
| 5 | 55 | 0.29 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 427 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 426 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 415 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5EIL · Computational design of a high-affinity metalloprotein homotrimer containing a metal… · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 5EIL · PDBe 5EIL
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