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HK97 bacteriophage capsid expansion intermediate-II model

Analyse HK97 bacteriophage capsid expansion intermediate-II model in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DDX
Type: protein
Length: 1,960 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein
UniProt: P49861
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 25% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Major capsid protein	protein	280	25% helix, 30% strand	P49861

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	957	0.79	0.81	137	empty
2	986	0.78	0.81	127	empty
3	1065	0.78	0.80	131	empty
4	800	0.78	0.82	93	empty
5	880	0.77	0.81	96	empty

Interfaces

7 interfaces between chains.

B–C · 1706 Å² buried · 38 hydrogen bonds · protein-protein
A–F · 1500 Å² buried · 45 hydrogen bonds · protein-protein
D–E · 1390 Å² buried · 44 hydrogen bonds · protein-protein
E–F · 1151 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1025 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3DDX · HK97 bacteriophage capsid Expansion Intermediate-II model · 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
Every structure of UniProt P49861
Elsewhere: RCSB PDB 3DDX · PDBe 3DDX · UniProt P49861

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