scPDB - 2q7h entry

Protein Data Bank Entry:

PDB ID : 2q7h

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2007-06-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyrrolysine--tRNA ligase
ID:	PYLS_METMA
AC:	Q8PWY1
Organism:	Methanosarcina mazei
Reign:	Archaea
TaxID:	192952
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	47.240
Number of residues:	56
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.471	799.875

% Hydrophobic	% Polar
40.51	59.49
According to VolSite

Ligand :

HET Code:	YLY
Formula:	C22H36N8O9P
Molecular weight:	587.543 g/mol
DrugBank ID:	-
Buried Surface Area:	79.08 %
Polar Surface area:	278.13 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
10.718	41.773	32.9753

Binding mode :

What is Poseview ?

2D View
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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
CAA	CB	LEU- 305	3.43	0	Hydrophobic	false
CAP	CD1	TYR- 306	3.8	0	Hydrophobic	false
O	NH2	ARG- 330	2.9	130.92	H-Bond (Protein Donor)	false
OAF	NH1	ARG- 330	2.82	150.46	H-Bond (Protein Donor)	false
OAF	NH2	ARG- 330	3.01	139.71	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 330	3.46	128.47	H-Bond (Protein Donor)	false
OAF	CZ	ARG- 330	3.33	0	Ionic (Protein Cationic)	false
N6	OE2	GLU- 332	3.11	135.87	H-Bond (Ligand Donor)	false
N1	N	LEU- 339	2.97	170.38	H-Bond (Protein Donor)	false
N6	O	LEU- 339	2.81	128.04	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 342	3.99	0	Hydrophobic	false
DuAr	DuAr	PHE- 342	3.72	0	Aromatic Face/Face	false
C5'	CE	MET- 344	3.93	0	Hydrophobic	false
OAD	ND2	ASN- 346	2.66	160.25	H-Bond (Protein Donor)	false
CAA	SG	CYS- 348	3.73	0	Hydrophobic	false
NAS	OH	TYR- 384	2.78	134.09	H-Bond (Protein Donor)	false
CAM	CZ	TYR- 384	4.14	0	Hydrophobic	false
O2'	O	GLU- 396	3.39	171.43	H-Bond (Ligand Donor)	false
OAI	OG	SER- 399	3.1	146.37	H-Bond (Protein Donor)	false
CAM	CG2	VAL- 401	3.96	0	Hydrophobic	false
CBF	CZ3	TRP- 417	4.27	0	Hydrophobic	false
O2'	N	GLY- 423	3	129.63	H-Bond (Protein Donor)	false
C2'	CD	ARG- 426	4.1	0	Hydrophobic	false
N3	O	HOH- 912	2.85	148.25	H-Bond (Protein Donor)	false
N	O	HOH- 1086	3.08	135.71	H-Bond (Ligand Donor)	false