Research workbench
Designed armadillo repeat protein YIIIM5AII in complex with peptide (KR)5
Analyse Designed armadillo repeat protein YIIIM5AII in complex with peptide (KR)5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AEI
- Type
- protein
- Length
- 875 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed armadillo repeat protein YIIIM5AII; KR5
- Ligands
- CA
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Designed armadillo repeat protein YIIIM5AII | protein | 281 | 74% helix, 0% strand | — |
| B, C | Designed armadillo repeat protein YIIIM5AII | protein | 282 | 75% helix, 0% strand | — |
| D, E, F | KR5 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 13 copies · chains A, B, C
- ACT · Acetate ion · additive · 5 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.73 | 0.82 | 63 | empty |
| 2 | 1009 | 0.72 | 0.76 | 96 | GOL |
Interfaces
9 interfaces between chains.
- B–C · 1454 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 1076 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1073 Ų buried · 33 hydrogen bonds · protein-protein
- B–E · 1068 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 305 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5AEI · Designed Armadillo repeat protein YIIIM5AII in complex with peptide (KR)5 · 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
- Elsewhere: RCSB PDB 5AEI · PDBe 5AEI
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