Research workbench
Crystal structure of CPSRP43 chromodomains 2 and 3 in complex with the ALB3 tail
Analyse Crystal structure of CPSRP43 chromodomains 2 and 3 in complex with the ALB3 tail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E4W
- Type
- protein
- Length
- 444 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin-1; Signal recognition particle 43 kda protein, chloroplastic; Inner membrane…
- UniProt
- P0AA27, O22265, Q8LBP4
- Ligands
- CA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin-1 | protein | 109 | 36% helix, 31% strand | P0AA27 |
| B | Thioredoxin-1 | protein | 108 | 35% helix, 30% strand | P0AA27 |
| C, D | Signal recognition particle 43 kda protein, chloroplastic | protein | 105 | 23% helix, 47% strand | O22265 |
| E | Inner membrane protein ALBINO3, chloroplastic | protein | 9 | 0% helix, 44% strand | Q8LBP4 |
| F | Inner membrane protein ALBINO3, chloroplastic | protein | 8 | 0% helix, 63% strand | Q8LBP4 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, A, D
- GOL · Glycerol · additive · 2 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.75 | 0.80 | 79 | empty |
| 2 | 87 | 0.58 | 0.87 | 23 | empty |
| 3 | 92 | 0.55 | 0.85 | 22 | empty |
| 4 | 97 | 0.43 | 0.79 | 17 | empty |
| 5 | 127 | 0.41 | 0.75 | 18 | empty |
Interfaces
8 interfaces between chains.
- C–E · 868 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 784 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 617 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 567 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 509 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5E4W · Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail · the same entry in another collection · chain F against F, TM-score 1.00
- P0AA27 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA27) · a predicted model of the same protein · chain B against A, TM-score 0.97
- O22265 · AlphaFold monomer V2.0 prediction for signal recognition particle 43 kda protein… · a predicted model of the same protein · chain C against A, TM-score 0.90
- Q8LBP4 · AlphaFold monomer V2.0 prediction for inner membrane protein ALBINO3, chloroplastic… · a predicted model of the same protein · chain F against A, TM-score 0.43
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 P0AA27
- Every structure of UniProt O22265
- Every structure of UniProt Q8LBP4
- Elsewhere: RCSB PDB 5E4W · PDBe 5E4W · UniProt P0AA27 · UniProt O22265 · UniProt Q8LBP4
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