scPDB - 1z2i entry

Protein Data Bank Entry:

PDB ID : 1z2i

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2005-03-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative malate dehydrogenase
ID:	Q7CRW4_AGRFC
AC:	Q7CRW4
Organism:	Agrobacterium fabrum )
Reign:	Bacteria
TaxID:	176299
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	14 %
D	86 %

Ligand binding site composition:

B-Factor:	20.659
Number of residues:	50
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.908	1609.875

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	64.82 %
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
2.23495	38.8645	8.47336

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
C4D	CG2	VAL- 50	3.53	0	Hydrophobic	false
N7N	O	GLY- 127	2.69	146.49	H-Bond (Ligand Donor)	false
O2D	N	ALA- 129	2.79	164.38	H-Bond (Protein Donor)	false
C5N	CB	THR- 165	3.5	0	Hydrophobic	false
C2D	CB	PRO- 167	4.37	0	Hydrophobic	false
C4N	CG	PRO- 167	3.85	0	Hydrophobic	false
C4B	CD1	LEU- 182	4.11	0	Hydrophobic	false
O3B	N	ASP- 183	3.28	170.01	H-Bond (Protein Donor)	false
C3D	CB	ASP- 183	4.48	0	Hydrophobic	false
O3D	OD2	ASP- 183	3.34	130.18	H-Bond (Ligand Donor)	false
O3D	OD1	ASP- 183	2.71	164.16	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 183	2.51	163.4	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 183	3.32	124.97	H-Bond (Ligand Donor)	false
C5B	CB	MET- 184	3.65	0	Hydrophobic	false
O1N	N	ALA- 185	2.7	173.32	H-Bond (Protein Donor)	false
C5N	CB	ALA- 185	4.24	0	Hydrophobic	false
C4B	CD1	PHE- 235	4.29	0	Hydrophobic	false
C1B	CD1	PHE- 235	3.95	0	Hydrophobic	false
O1A	NZ	LYS- 236	3.79	0	Ionic (Protein Cationic)	false
O1N	NZ	LYS- 236	2.91	0	Ionic (Protein Cationic)	false
O1N	NZ	LYS- 236	2.91	152.55	H-Bond (Protein Donor)	false
O2B	N	GLY- 318	3.31	156.49	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 320	3.04	170.85	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 320	3.88	0	Ionic (Protein Cationic)	false
O2B	OE2	GLU- 321	2.7	152.9	H-Bond (Ligand Donor)	false
O2B	O	HOH- 784	3.23	160.47	H-Bond (Protein Donor)	false