Research workbench

Kinetically trapped pseudomonas-phage PAP3 portal protein - delta barrel mutant class-2

Analyse Kinetically trapped pseudomonas-phage PAP3 portal protein - delta barrel mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SZ4
Type: protein
Length: 5,973 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Portal protein
UniProt: Q8H9R8
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 4 distinct chains · 45% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
k, j, l, a, b, c, d, e, f	Portal protein	protein	505	44% helix, 9% strand	Q8H9R8
i	Portal protein	protein	471	45% helix, 8% strand	Q8H9R8
h	Portal protein	protein	467	45% helix, 7% strand	Q8H9R8
g	Portal protein	protein	490	45% helix, 8% strand	Q8H9R8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1169	0.89	0.90	163	empty
2	802	0.88	0.91	125	empty
3	1070	0.87	0.88	114	empty
4	757	0.87	0.90	107	empty
5	940	0.87	0.88	99	empty

Interfaces

13 interfaces between chains.

a–b · 3905 Å² buried · 49 hydrogen bonds · protein-protein
k–j · 3777 Å² buried · 42 hydrogen bonds · protein-protein
l–a · 3772 Å² buried · 55 hydrogen bonds · protein-protein
b–c · 3757 Å² buried · 42 hydrogen bonds · protein-protein
k–l · 3754 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

7SZ4 · Kinetically trapped Pseudomonas-phage PaP3 portal protein - delta barrel mutant class-2 · 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 Q8H9R8
Elsewhere: RCSB PDB 7SZ4 · PDBe 7SZ4 · UniProt Q8H9R8

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