scPDB - 5exd entry

Protein Data Bank Entry:

PDB ID : 5exd

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2015-11-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Oxalate oxidoreductase subunit alpha	Oxalate oxidoreductase subunit beta
ID:	OORA_MOOTA	OORB_MOOTA
AC:	Q2RI41	Q2RI42
Organism:	Moorella thermoacetica
Reign:	Bacteria
TaxID:	264732
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
G	31 %
J	2 %
I	67 %

Ligand binding site composition:

B-Factor:	25.761
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.305	270.000

% Hydrophobic	% Polar
57.50	42.50
According to VolSite

Ligand :

HET Code:	TPP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	-
Buried Surface Area:	83.58 %
Polar Surface area:	225.32 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-38.7782	66.1431	-30.2387

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
CM4	CE2	TYR- 28	4.33	0	Hydrophobic	false
CM4	CG	PRO- 29	4.13	0	Hydrophobic	false
C5'	CD1	ILE- 30	3.53	0	Hydrophobic	false
S1	CG2	THR- 50	3.54	0	Hydrophobic	false
O1B	N	CYS- 52	2.96	143.18	H-Bond (Protein Donor)	false
O2B	N	CYS- 52	2.83	141.02	H-Bond (Protein Donor)	false
CM2	CG2	ILE- 74	3.72	0	Hydrophobic	false
CM4	CD1	ILE- 74	3.95	0	Hydrophobic	false
C7	CD1	ILE- 74	3.53	0	Hydrophobic	false
CM2	CG2	THR- 75	3.87	0	Hydrophobic	false
CM2	CG2	VAL- 83	4.26	0	Hydrophobic	false
CM2	CB	TYR- 87	4.34	0	Hydrophobic	false
O2A	N	GLY- 111	3.28	164.04	H-Bond (Protein Donor)	false
O1A	N	GLY- 112	3.1	136.04	H-Bond (Protein Donor)	false
CM2	CD1	ILE- 116	4.31	0	Hydrophobic	false
O1B	OH	TYR- 136	2.5	143.79	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 138	3	151.7	H-Bond (Protein Donor)	false
CM4	CD1	TYR- 141	3.63	0	Hydrophobic	false
C7	CD1	TYR- 141	3.74	0	Hydrophobic	false
O3B	N	ALA- 142	2.97	160.88	H-Bond (Protein Donor)	false
S1	CB	ASN- 143	3.91	0	Hydrophobic	false
C6	CB	ASN- 143	4.01	0	Hydrophobic	false
O2B	N	ASN- 143	3.06	149.31	H-Bond (Protein Donor)	false
S1	CG2	THR- 144	4.23	0	Hydrophobic	false
CM4	CG2	THR- 144	3.74	0	Hydrophobic	false
C6	CG2	THR- 144	4.37	0	Hydrophobic	false
O2A	MG	MG- 403	2.11	0	Metal Acceptor	false
O3B	MG	MG- 403	2.02	0	Metal Acceptor	false