scPDB - 1x7d entry

Protein Data Bank Entry:

PDB ID : 1x7d

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2004-08-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative ornithine cyclodeaminase
ID:	Q88H32_PSEPK
AC:	Q88H32
Organism:	Pseudomonas putida
Reign:	Bacteria
TaxID:	160488
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	9 %
B	91 %

Ligand binding site composition:

B-Factor:	11.803
Number of residues:	61
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	2
Water Molecules:	5
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
1.031	550.125

% Hydrophobic	% Polar
52.76	47.24
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	74.21 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-4.7248	33.9185	15.6961

Binding mode :

What is Poseview ?

2D View
3D View

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
O2A	OG1	THR- 84	2.61	169.44	H-Bond (Protein Donor)	false
C2D	CG2	VAL- 85	4.1	0	Hydrophobic	false
C6N	CG2	VAL- 85	4.1	0	Hydrophobic	false
C4N	CG2	THR- 109	4.16	0	Hydrophobic	false
O7N	NH2	ARG- 112	2.9	130.1	H-Bond (Protein Donor)	false
C4N	CG2	THR- 113	3.65	0	Hydrophobic	false
O1A	N	ALA- 139	2.93	177.75	H-Bond (Protein Donor)	false
O1N	NE2	GLN- 140	3.13	171.05	H-Bond (Protein Donor)	false
O2N	N	GLN- 140	2.88	169.6	H-Bond (Protein Donor)	false
C5D	CG	GLN- 140	4.11	0	Hydrophobic	false
C5N	CG	GLN- 140	3.9	0	Hydrophobic	false
O3B	OD2	ASP- 161	2.73	173.93	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 161	2.7	164.49	H-Bond (Ligand Donor)	false
N3A	N	THR- 162	3.49	160.23	H-Bond (Protein Donor)	false
C5D	CB	VAL- 201	4.41	0	Hydrophobic	false
O3D	O	THR- 202	3.13	172.21	H-Bond (Ligand Donor)	false
C5B	CB	ALA- 203	3.61	0	Hydrophobic	false
C3D	CB	ALA- 203	3.67	0	Hydrophobic	false
O4B	N	ALA- 203	3.36	145.46	H-Bond (Protein Donor)	false
N7N	O	VAL- 225	3.12	164.51	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 228	2.71	167.95	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 228	3.45	131.28	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 232	2.53	137.53	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 232	3.43	145.55	H-Bond (Protein Donor)	false
N7N	OG	SER- 293	3.07	144.63	H-Bond (Ligand Donor)	false
C3B	CD	LYS- 331	4.22	0	Hydrophobic	false
O3B	NZ	LYS- 331	2.94	151.02	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 331	3.22	121.62	H-Bond (Protein Donor)	false
O2D	NE	ORN- 1102	2.88	133.87	H-Bond (Protein Donor)	false
O1A	O	HOH- 1516	2.82	179.96	H-Bond (Protein Donor)	false
O2N	O	HOH- 3165	2.76	172.01	H-Bond (Protein Donor)	false