MolNFT v1 · #168111 · protein

Structure of the globular C-terminal domain of P. aeruginosa lpop

6W5Q · Peptidoglycan synthase activator lpop: “Structure of the globular C-terminal domain of P. aeruginosa lpop”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.76). MolNFT v1 #168111 on GenesisL1: 3D structure…

PDB: 6W5Q
Type: protein
Length: 834 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidoglycan synthase activator lpop
UniProt: Q9HV97
Ligands: SO4
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 7 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidoglycan synthase activator lpop	protein	106	81% helix, 0% strand	Q9HV97
B, E	Peptidoglycan synthase activator lpop	protein	104	79% helix, 0% strand	Q9HV97
C	Peptidoglycan synthase activator lpop	protein	104	82% helix, 0% strand	Q9HV97
D	Peptidoglycan synthase activator lpop	protein	105	80% helix, 0% strand	Q9HV97
F	Peptidoglycan synthase activator lpop	protein	102	79% helix, 0% strand	Q9HV97
G	Peptidoglycan synthase activator lpop	protein	103	81% helix, 0% strand	Q9HV97
H	Peptidoglycan synthase activator lpop	protein	106	78% helix, 0% strand	Q9HV97

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains A, B, G, C, D, F, H
PGE · Triethylene glycol · additive · chains D, E, H

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	747	0.76	0.80	55	empty
2	619	0.72	0.79	53	empty
3	677	0.66	0.75	60	empty
4	227	0.53	0.77	36	PGE
5	62	0.41	0.80	12	empty

Interfaces

9 interfaces between chains.

B–C · 716 Å² buried · 9 hydrogen bonds · protein-protein
F–G · 659 Å² buried · 5 hydrogen bonds · protein-protein
E–H · 566 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 498 Å² buried · 10 hydrogen bonds · protein-protein
B–G · 300 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6W5Q · Structure of the globular C-terminal domain of P. aeruginosa LpoP · 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 Q9HV97
Elsewhere: RCSB PDB 6W5Q · PDBe 6W5Q · UniProt Q9HV97

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