scPDB - 3umv entry

Protein Data Bank Entry:

PDB ID : 3umv

Resolution :1.710 Å

Experimental Method : X-ray

Deposition Date : 2011-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxyribodipyrimidine photo-lyase
ID:	PHR_ORYSJ
AC:	Q6F6A2
Organism:	Oryza sativa subsp. japonica
Reign:	Eukaryota
TaxID:	39947
EC Number:	4.1.99.3

Chains:

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

Ligand binding site composition:

B-Factor:	16.793
Number of residues:	54
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.829	1005.750

% Hydrophobic	% Polar
39.93	60.07
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	73.78 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
17.4153	-3.17258	14.6172

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
O1A	OH	TYR- 268	2.55	175.86	H-Bond (Protein Donor)	false
O2A	OG	SER- 282	2.8	146.64	H-Bond (Protein Donor)	false
O2A	N	SER- 282	2.83	157.09	H-Bond (Protein Donor)	false
O2P	N	GLY- 283	2.89	149.69	H-Bond (Protein Donor)	false
O1P	N	LEU- 284	3.31	123.17	H-Bond (Protein Donor)	false
C3B	CB	SER- 285	4.39	0	Hydrophobic	false
C5'	CB	SER- 285	3.51	0	Hydrophobic	false
O1P	N	SER- 285	2.94	137.51	H-Bond (Protein Donor)	false
C3B	CD1	LEU- 288	4.31	0	Hydrophobic	false
C5B	CE2	PHE- 316	3.82	0	Hydrophobic	false
C1B	CB	GLU- 319	4.44	0	Hydrophobic	false
C4B	CD1	LEU- 320	4.22	0	Hydrophobic	false
C1B	CB	ARG- 324	4.22	0	Hydrophobic	false
O2P	NZ	LYS- 390	2.81	153.6	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 390	2.81	0	Ionic (Protein Cationic)	false
N5	NH1	ARG- 396	3.21	133	H-Bond (Protein Donor)	false
C6	CD	ARG- 396	3.83	0	Hydrophobic	false
C9A	CD	ARG- 396	3.69	0	Hydrophobic	false
C8	CB	ARG- 396	3.55	0	Hydrophobic	false
C8M	CG	MET- 397	3.73	0	Hydrophobic	false
C7M	CE3	TRP- 399	4.34	0	Hydrophobic	false
C7M	CB	ALA- 400	3.74	0	Hydrophobic	false
O4	ND2	ASN- 421	2.93	167.07	H-Bond (Protein Donor)	false
N3	O	ASP- 427	2.7	161.59	H-Bond (Ligand Donor)	false
C6	SG	CYS- 437	4.37	0	Hydrophobic	false
C7M	SG	CYS- 437	4.2	0	Hydrophobic	false
O4'	O	HOH- 720	2.7	169.28	H-Bond (Protein Donor)	false