Research workbench
Crystal structure of ACAP1 C-portion mutant S554D fused with integrin BETA1 peptide
Analyse Crystal structure of ACAP1 C-portion mutant S554D fused with integrin BETA1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T9K
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arf-gap with coiled-coil, ank repeat and pH domain- containing protein 1,PEPTIDE from…
- UniProt
- Q15027, P05556
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arf-gap with coiled-coil, ank repeat and pH domain- containing protein 1,PEPTIDE from integrin beta-1 | protein | 281 | 48% helix, 4% strand | Q15027, P05556 |
| B | Arf-gap with coiled-coil, ank repeat and pH domain- containing protein 1,PEPTIDE from integrin beta-1 | protein | 273 | 48% helix, 4% strand | Q15027, P05556 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.54 | 0.82 | 22 | empty |
| 2 | 322 | 0.53 | 0.75 | 34 | empty |
| 3 | 92 | 0.47 | 0.80 | 19 | empty |
| 4 | 93 | 0.46 | 0.80 | 16 | empty |
| 5 | 69 | 0.40 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3T9K · Crystal Structure of ACAP1 C-portion mutant S554D fused with integrin beta1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q15027 · AlphaFold monomer V2.0 prediction for arf-gap with coiled-coil, ank repeat and pH… · a predicted model of the same protein · chain B against A, TM-score 0.97
- P05556 · AlphaFold monomer V2.0 prediction for integrin beta-1 (P05556) · a predicted model of the same protein · chain B against A, TM-score 0.33
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 Q15027
- Every structure of UniProt P05556
- Elsewhere: RCSB PDB 3T9K · PDBe 3T9K · UniProt Q15027 · UniProt P05556
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