scPDB - 3zlm entry

Protein Data Bank Entry:

PDB ID : 3zlm

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-02-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenosine monophosphate-protein transferase NmFic
ID:	NMFIC_NEIMB
AC:	Q7DDR9
Organism:	Neisseria meningitidis serogroup B
Reign:	Bacteria
TaxID:	122586
EC Number:	2.7.7.n1

Chains:

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

Ligand binding site composition:

B-Factor:	42.729
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.481	617.625

% Hydrophobic	% Polar
49.18	50.82
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	68.16 %
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
-46.4268	-54.7423	-18.1891

Binding mode :

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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
N3	ND2	ASN- 104	3.01	167.07	H-Bond (Protein Donor)	false
O4'	NE2	HIS- 107	2.89	154.4	H-Bond (Protein Donor)	false
O2B	N	GLY- 112	3.15	132.55	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 113	2.85	160.61	H-Bond (Protein Donor)	false
O2A	N	ASN- 113	3.03	154.79	H-Bond (Protein Donor)	false
O3A	N	GLY- 114	2.72	164.05	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 115	3.68	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 115	3.71	0	Ionic (Protein Cationic)	false
O1B	NE	ARG- 115	2.81	161.06	H-Bond (Protein Donor)	false
O1B	N	ARG- 115	2.82	153.15	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 115	2.89	139.98	H-Bond (Protein Donor)	false
O1G	NH2	ARG- 118	2.95	147.02	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 118	3.01	143.68	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 118	2.85	137.22	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 118	2.94	138.8	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 118	3.42	0	Ionic (Protein Cationic)	false
C2'	CD2	LEU- 144	4.06	0	Hydrophobic	false
C2'	CB	MET- 147	4.19	0	Hydrophobic	false
O2B	MG	MG- 301	2.29	0	Metal Acceptor	false
O1A	MG	MG- 301	2.53	0	Metal Acceptor	false