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Crystal structure of the phage vqma-dpo complex

Analyse Crystal structure of the phage vqma-dpo complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DWM
Type: protein
Length: 436 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator
UniProt: A2I306
Ligands: A1U
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulator	protein	218	45% helix, 19% strand	A2I306
B	Transcriptional regulator	protein	218	47% helix, 21% strand	A2I306

Ligands and binding sites

A1U · 3,5-dimethylpyrazin-2-ol · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1047	0.79	0.81	91	empty
2	54	0.73	0.99	18	A1U
3	55	0.73	0.99	19	A1U
4	94	0.50	0.82	17	empty
5	86	0.33	0.73	22	empty

Interfaces

1 interface between chains.

A–B · 2395 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

7DWM · Crystal structure of the phage VqmA-DPO complex · 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 A2I306
Elsewhere: RCSB PDB 7DWM · PDBe 7DWM · UniProt A2I306

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