Research workbench

Cell wall binding domain of the staphylococcal phage 2638A endolysin

Analyse Cell wall binding domain of the staphylococcal phage 2638A endolysin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AQH
Type: protein
Length: 744 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ORF007
UniProt: Q4ZD58
Pockets: 8 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, C, G, H, B, E, F	ORF007	protein	93	0% helix, 56% strand	Q4ZD58

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, H, E, D, G

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	371	0.62	0.78	37	empty
2	357	0.59	0.77	39	empty
3	109	0.41	0.76	18	empty
4	66	0.35	0.77	14	empty
5	58	0.32	0.75	12	empty

Interfaces

11 interfaces between chains.

A–E · 493 Å² buried · 6 hydrogen bonds · protein-protein
C–G · 490 Å² buried · 4 hydrogen bonds · protein-protein
H–E · 488 Å² buried · 3 hydrogen bonds · protein-protein
D–G · 476 Å² buried · 3 hydrogen bonds · protein-protein
H–F · 474 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7AQH · Cell wall binding domain of the Staphylococcal phage 2638A endolysin · the same entry in another collection · chain E against E, 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 Q4ZD58
Elsewhere: RCSB PDB 7AQH · PDBe 7AQH · UniProt Q4ZD58

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.