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Kinetically trapped pseudomonas-phage PAP3 portal protein - full length

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

PDB: 7SXK
Type: protein
Length: 6,513 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Portal protein
UniProt: Q8H9R8
Pockets: 20 · best druggability 0.91

Structure

electron microscopy · 11 distinct chains · 45% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	Portal protein	protein	568	45% helix, 9% strand	Q8H9R8
a	Portal protein	protein	558	46% helix, 7% strand	Q8H9R8
l	Portal protein	protein	555	44% helix, 7% strand	Q8H9R8
k	Portal protein	protein	565	46% helix, 7% strand	Q8H9R8
j	Portal protein	protein	578	48% helix, 7% strand	Q8H9R8
i	Portal protein	protein	564	46% helix, 7% strand	Q8H9R8
h	Portal protein	protein	559	46% helix, 6% strand	Q8H9R8
c, d	Portal protein	protein	569	47% helix, 6% strand	Q8H9R8
e	Portal protein	protein	562	46% helix, 7% strand	Q8H9R8
f	Portal protein	protein	518	44% helix, 7% strand	Q8H9R8
g	Portal protein	protein	348	34% helix, 3% 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	1136	0.91	0.93	155	empty
2	961	0.88	0.89	114	empty
3	676	0.88	0.92	92	empty
4	754	0.87	0.91	92	empty
5	815	0.85	0.88	109	empty

Interfaces

14 interfaces between chains.

c–d · 5207 Å² buried · 53 hydrogen bonds · protein-protein
d–e · 5126 Å² buried · 56 hydrogen bonds · protein-protein
b–c · 5115 Å² buried · 38 hydrogen bonds · protein-protein
k–j · 5099 Å² buried · 40 hydrogen bonds · protein-protein
b–a · 5012 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7SXK · Kinetically trapped Pseudomonas-phage PaP3 portal protein - Full Length · the same entry in another collection · chain b against b, 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 7SXK · PDBe 7SXK · UniProt Q8H9R8

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