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Cyanophage PAM1 capsid asymmetric unit

Analyse Cyanophage PAM1 capsid asymmetric unit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EEL
Type: protein
Length: 3,535 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid proteins; Cement (decoration) proteins
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 2 distinct chains · 11% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Major capsid proteins	protein	365	16% helix, 28% strand	—
H, I, J, K, L, M, N	Cement (decoration) proteins	protein	140	0% helix, 36% strand	—

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	531	0.80	0.86	38	empty
2	546	0.80	0.86	42	empty
3	718	0.76	0.81	81	empty
4	512	0.74	0.82	71	empty
5	593	0.73	0.80	80	empty

Interfaces

38 interfaces between chains.

D–E · 2927 Å² buried · 24 hydrogen bonds · protein-protein
A–F · 2787 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2763 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2669 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 2445 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

7EEL · Cyanophage Pam1 capsid asymmetric unit · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 7EEL · PDBe 7EEL

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