Research workbench

TarP-6RboP-(CH2)6NH2

Analyse TarP-6RboP-(CH2)6NH2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HNQ
Type: protein
Length: 3,772 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: Staphylococcus aureus subsp. aureus N315
Molecule: Probable ss-1,3-N-acetylglucosaminyltransferase
UniProt: A0A0H3JNB0
Ligands: FQ8, MG, CL
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · resolution 2.4 · 8 distinct chains · 45% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, H	Probable ss-1,3-N-acetylglucosaminyltransferase	protein	318	45% helix, 14% strand	A0A0H3JNB0
C	Probable ss-1,3-N-acetylglucosaminyltransferase	protein	312	46% helix, 15% strand	A0A0H3JNB0
F	Probable ss-1,3-N-acetylglucosaminyltransferase	protein	317	45% helix, 15% strand	A0A0H3JNB0
O	Probable ss-1,3-N-acetylglucosaminyltransferase	protein	316	45% helix, 15% strand	A0A0H3JNB0
P	Probable ss-1,3-N-acetylglucosaminyltransferase	protein	300	45% helix, 15% strand	A0A0H3JNB0
E, A	Probable ss-1,3-N-acetylglucosaminyltransferase	protein	317	45% helix, 15% strand	A0A0H3JNB0
G, D, I	Probable ss-1,3-N-acetylglucosaminyltransferase	protein	314	46% helix, 15% strand	A0A0H3JNB0
Q	Probable ss-1,3-N-acetylglucosaminyltransferase	protein	315	43% helix, 14% strand	A0A0H3JNB0

Ligands and binding sites

FQ8 · [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] [(2~{R},3~{R},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentoxy]phosphoryl]oxy-pentyl] hydrogen phosphate · ligand · 12 copies · chains B, C, F, O, P, E, G, Q, A, D, H, I
MG · Magnesium ion · metal · 4 copies · chains B, C, F, E, G, Q, P, A, D, H, I
CL · Chloride ion · ion · 17 copies · chains B, E, F, G, Q, A, H, D, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	614	0.73	0.80	91	empty
2	257	0.64	0.82	35	empty
3	119	0.62	0.87	21	empty
4	132	0.62	0.86	22	empty
5	107	0.61	0.87	23	empty

Interfaces

22 interfaces between chains.

B–E · 605 Å² buried · 5 hydrogen bonds · protein-protein
O–H · 570 Å² buried · 3 hydrogen bonds · protein-protein
B–F · 560 Å² buried · 3 hydrogen bonds · protein-protein
A–H · 529 Å² buried · 6 hydrogen bonds · protein-protein
E–Q · 494 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6HNQ · Tarp-6RBOP-(CH2)6NH2 · 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 A0A0H3JNB0
Elsewhere: RCSB PDB 6HNQ · PDBe 6HNQ · UniProt A0A0H3JNB0

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