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Coliphage K5A lyase

Analyse Coliphage K5A lyase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2X3H
Type: protein
Length: 1,494 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: K5 lyase
EC: 4.2.2.7
UniProt: Q9AZ47
Ligands: BR
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	K5 lyase (EC 4.2.2.7)	protein	498	5% helix, 48% strand	Q9AZ47

Ligands and binding sites

BR · Bromide ion · ion · 12 copies · chains A, B, C

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	564	0.83	0.89	90	empty
2	84	0.76	0.98	23	empty
3	290	0.63	0.81	33	empty
4	203	0.62	0.83	24	empty
5	177	0.61	0.83	24	empty

Interfaces

3 interfaces between chains.

B–C · 5908 Å² buried · 116 hydrogen bonds · protein-protein
A–C · 5864 Å² buried · 119 hydrogen bonds · protein-protein
A–B · 5859 Å² buried · 115 hydrogen bonds · protein-protein

Compared structures

2X3H · Coliphage K5A lyase · 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 Q9AZ47
Elsewhere: RCSB PDB 2X3H · PDBe 2X3H · UniProt Q9AZ47

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