MolNFT v1 · #79653 · protein

Crystal structure of ACAP1 C-portion mutant S554D fused with integrin BETA1 peptide

3T9K · Arf-gap with coiled-coil, ank repeat and pH domain…: “Crystal structure of ACAP1 C-portion mutant S554D fused with integrin BETA1 peptide”. X-ray diffraction, 2 ligands (ZN, SO4), 5 pockets (best druggability 0.54). MolNFT v1 #79653…

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

ZN · Zinc ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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.

Pocket	Volume (Å³)	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 Å² 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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