scPDB - 3l04 entry

Protein Data Bank Entry:

PDB ID : 3l04

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-acetylornithine carbamoyltransferase
ID:	AOTC_XANCP
AC:	Q8P8J2
Organism:	Xanthomonas campestris pv. campestris
Reign:	Bacteria
TaxID:	190485
EC Number:	2.1.3.9

Chains:

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

Ligand binding site composition:

B-Factor:	30.422
Number of residues:	27
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.069	303.750

% Hydrophobic	% Polar
56.67	43.33
According to VolSite

Ligand :

HET Code:	SN0
Formula:	C9H13NO5
Molecular weight:	215.203 g/mol
DrugBank ID:	DB08554
Buried Surface Area:	58.07 %
Polar Surface area:	109.36 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
110.421	41.3158	82.2073

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
CB	CZ	PHE- 114	3.76	0	Hydrophobic	false
O	OE1	GLU- 144	2.5	145.96	H-Bond (Protein Donor)	false
OD1	NE2	HIS- 180	2.7	164.47	H-Bond (Protein Donor)	false
C2	CD1	LEU- 184	4.03	0	Hydrophobic	false
C3	CD2	LEU- 184	4.23	0	Hydrophobic	false
CG	CG2	VAL- 188	4.15	0	Hydrophobic	false
O	NZ	LYS- 252	3.8	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 252	2.61	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 252	2.61	157.5	H-Bond (Protein Donor)	false
CD	SG	CYS- 294	3.57	0	Hydrophobic	false
C2	CG	PRO- 296	4.42	0	Hydrophobic	false
OD1	NE	ARG- 298	2.84	167.53	H-Bond (Protein Donor)	false
OD2	NH2	ARG- 298	2.84	167.4	H-Bond (Protein Donor)	false
OD1	CZ	ARG- 298	3.62	0	Ionic (Protein Cationic)	false
OD2	CZ	ARG- 298	3.71	0	Ionic (Protein Cationic)	false
N1	O	HOH- 383	3.02	167.43	H-Bond (Ligand Donor)	false