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Crystal Structure of the Bacteriophage phi29 gene product 12 C-terminal fragment

Analyse Crystal Structure of the Bacteriophage phi29 gene product 12 C-terminal fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GQH
Type: protein
Length: 489 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.8
Source: Bacillus phage phi29
Molecule: Preneck appendage protein
UniProt: B3VMP8
Pockets: 9 · best druggability 0.58

Structure

x-ray diffraction · resolution 1.8 · 1 distinct chain · 2% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Preneck appendage protein	protein	163	2% helix, 46% strand	B3VMP8

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	376	0.58	0.75	27	empty
2	134	0.50	0.79	27	empty
3	82	0.48	0.82	17	empty
4	89	0.48	0.82	22	empty
5	103	0.34	0.73	20	empty

Interfaces

3 interfaces between chains.

A–B · 1132 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 1119 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1083 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3GQH · Crystal structure of the bacteriophage PHI29 gene product 12 C- terminal fragment · 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 B3VMP8
Elsewhere: RCSB PDB 3GQH · PDBe 3GQH · UniProt B3VMP8

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