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Crystal structure of swapped human nck SH3.1 domain, 1.8A, triclinic

Analyse Crystal structure of swapped human nck SH3.1 domain, 1.8A, triclinic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5QU6
Type: protein
Length: 1,546 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytoplasmic protein NCK1
UniProt: P16333
Pockets: 19 · best druggability 0.74

Structure

x-ray diffraction · 14 distinct chains · 7% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, M, P, R, T	Cytoplasmic protein NCK1	protein	55	5% helix, 44% strand	P16333
C	Cytoplasmic protein NCK1	protein	55	5% helix, 44% strand	P16333
E, L	Cytoplasmic protein NCK1	protein	59	5% helix, 44% strand	P16333
F	Cytoplasmic protein NCK1	protein	57	5% helix, 44% strand	P16333
G, Q, S	Cytoplasmic protein NCK1	protein	56	11% helix, 41% strand	P16333
H, J	Cytoplasmic protein NCK1	protein	58	10% helix, 43% strand	P16333
I, N	Cytoplasmic protein NCK1	protein	56	5% helix, 45% strand	P16333
K, O	Cytoplasmic protein NCK1	protein	58	5% helix, 38% strand	P16333
U	Cytoplasmic protein NCK1	protein	53	6% helix, 43% strand	P16333
V	Cytoplasmic protein NCK1	protein	53	11% helix, 40% strand	P16333
W	Cytoplasmic protein NCK1	protein	55	5% helix, 40% strand	P16333
X, Z, 1	Cytoplasmic protein NCK1	protein	54	11% helix, 41% strand	P16333
Y	Cytoplasmic protein NCK1	protein	50	6% helix, 38% strand	P16333
2	Cytoplasmic protein NCK1	protein	46	7% helix, 41% strand	P16333

Pockets

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1165	0.74	0.77	120	empty
2	843	0.71	0.76	71	empty
3	397	0.67	0.80	43	empty
4	463	0.65	0.78	57	empty
5	214	0.59	0.81	39	empty

Interfaces

71 interfaces between chains.

Q–R · 2193 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 2190 Å² buried · 25 hydrogen bonds · protein-protein
S–T · 2182 Å² buried · 30 hydrogen bonds · protein-protein
G–H · 2156 Å² buried · 32 hydrogen bonds · protein-protein
O–P · 2148 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

P16333 · AlphaFold monomer V2.0 prediction for cytoplasmic protein NCK1 (P16333) · a predicted model of the same protein · chain U against A, TM-score 0.59

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 P16333
Elsewhere: RCSB PDB 5QU6 · PDBe 5QU6 · UniProt P16333

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