scPDB - 3gvi entry

Protein Data Bank Entry:

PDB ID : 3gvi

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2009-03-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase
ID:	MDH_BRUA2
AC:	Q2YLR9
Organism:	Brucella abortus
Reign:	Bacteria
TaxID:	359391
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.356
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.089	914.625

% Hydrophobic	% Polar
42.44	57.56
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	50.49 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
4.97056	69.9407	22.3791

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
O1A	N	MET- 13	3.07	166.93	H-Bond (Protein Donor)	false
O3B	N	ILE- 14	2.89	164.32	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 34	3.41	124.91	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 34	3.48	125.73	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 34	2.62	156.68	H-Bond (Ligand Donor)	false
N6	OE1	GLN- 102	2.94	157.54	H-Bond (Ligand Donor)	false
O3B	O	HOH- 360	2.55	171.19	H-Bond (Protein Donor)	false