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Crystal structure of a PB1 complex

Analyse Crystal structure of a PB1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MJS
Type: protein
Length: 2,060 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein kinase C zeta type; Sequestosome-1
EC: 2.7.11.13
UniProt: P09217, Q13501
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 9 distinct chains · 25% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M, O, Q, S, U, W	Protein kinase C zeta type (EC 2.7.11.13)	protein	88	27% helix, 38% strand	P09217
B	Sequestosome-1	protein	82	26% helix, 33% strand	Q13501
D, F, N, T	Sequestosome-1	protein	83	24% helix, 37% strand	Q13501
H, R	Sequestosome-1	protein	84	25% helix, 40% strand	Q13501
J	Sequestosome-1	protein	87	25% helix, 43% strand	Q13501
L	Sequestosome-1	protein	86	24% helix, 44% strand	Q13501
P	Sequestosome-1	protein	81	21% helix, 31% strand	Q13501
V	Sequestosome-1	protein	80	24% helix, 35% strand	Q13501
X	Sequestosome-1	protein	88	24% helix, 44% strand	Q13501

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 4 copies · chains H, M, K, O, X

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	650	0.74	0.80	75	empty
2	775	0.72	0.77	87	EDO
3	639	0.71	0.79	76	empty
4	621	0.70	0.78	68	empty
5	785	0.69	0.76	89	EDO

Interfaces

38 interfaces between chains.

S–T · 628 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 617 Å² buried · 17 hydrogen bonds · protein-protein
U–V · 607 Å² buried · 15 hydrogen bonds · protein-protein
M–N · 607 Å² buried · 14 hydrogen bonds · protein-protein
O–X · 606 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4MJS · crystal structure of a PB1 complex · the same entry in another collection · chain K against K, 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
Every structure of UniProt P09217
Every structure of UniProt Q13501
Elsewhere: RCSB PDB 4MJS · PDBe 4MJS · UniProt P09217 · UniProt Q13501

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