scPDB - 4cvm entry

Protein Data Bank Entry:

PDB ID : 4cvm

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2014-03-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
ID:	Q9HVZ7_PSEAE
AC:	Q9HVZ7
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	29.495
Number of residues:	30
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
1.278	1231.875

% Hydrophobic	% Polar
43.56	56.44
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	47.94 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
20.531	-30.8627	-9.55787

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C1'	CB	SER- 111	4.24	0	Hydrophobic	false
N1	OG	SER- 111	3.44	137.85	H-Bond (Protein Donor)	false
N3	OG	SER- 111	3.21	147.07	H-Bond (Protein Donor)	false
O3A	N	GLY- 112	3.01	150.61	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 113	2.7	171.48	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 113	2.69	148.01	H-Bond (Protein Donor)	false
O1B	N	LYS- 113	2.92	152.12	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 113	2.7	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 113	3.67	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 113	2.69	0	Ionic (Protein Cationic)	false
O2B	N	THR- 114	2.9	150.96	H-Bond (Protein Donor)	false
O1A	N	THR- 115	2.95	144.75	H-Bond (Protein Donor)	false
O1A	OG1	THR- 115	2.56	159.52	H-Bond (Protein Donor)	false
O2G	ND2	ASN- 140	2.85	147.04	H-Bond (Protein Donor)	false
N7	ND2	ASN- 292	2.96	176.01	H-Bond (Protein Donor)	false
N6	OD1	ASN- 292	2.88	157.12	H-Bond (Ligand Donor)	false
O2B	MG	MG- 1457	2.58	0	Metal Acceptor	false
O2A	MG	MG- 1457	2.76	0	Metal Acceptor	false
O2G	MG	MG- 1458	2.11	0	Metal Acceptor	false
O2B	MG	MG- 1458	2.08	0	Metal Acceptor	false
N6	O	HOH- 2027	3.01	153	H-Bond (Ligand Donor)	false