scPDB - 3zid entry

Protein Data Bank Entry:

PDB ID : 3zid

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tubulin-like protein CetZ
ID:	CETZ_METTP
AC:	A0B5R2
Organism:	Methanosaeta thermophila
Reign:	Archaea
TaxID:	349307
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.614
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.087	415.125

% Hydrophobic	% Polar
30.08	69.92
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	75.5 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
20.2119	-14.9444	-13.9414

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
O2B	N	GLN- 11	2.87	175.53	H-Bond (Protein Donor)	false
O2A	N	CYS- 12	2.96	169.32	H-Bond (Protein Donor)	false
C1'	CB	CYS- 12	4.3	0	Hydrophobic	false
O5'	OG	SER- 111	2.68	149.73	H-Bond (Protein Donor)	false
O4'	OG	SER- 111	3.26	129.45	H-Bond (Protein Donor)	false
C1'	CB	SER- 111	4.33	0	Hydrophobic	false
C4'	CB	SER- 111	3.62	0	Hydrophobic	false
C4'	CB	SER- 113	4.09	0	Hydrophobic	false
O3B	N	GLY- 115	2.95	140.37	H-Bond (Protein Donor)	false
O1B	N	THR- 116	3.45	123.19	H-Bond (Protein Donor)	false
O3B	N	THR- 116	2.89	172.96	H-Bond (Protein Donor)	false
O1B	N	GLY- 117	2.79	162.32	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 148	2.76	162.06	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 148	3.35	122.99	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 148	2.61	160.26	H-Bond (Ligand Donor)	false
C5'	CZ	TYR- 152	4.38	0	Hydrophobic	false
C3'	CE2	TYR- 152	4.22	0	Hydrophobic	false
N2	OD1	ASN- 176	2.93	155.59	H-Bond (Ligand Donor)	false
N3	ND2	ASN- 176	3.09	167.22	H-Bond (Protein Donor)	false
O2'	OH	TYR- 190	2.71	144.84	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 190	3.66	0	Aromatic Face/Face	false
C2'	CZ	TYR- 190	4	0	Hydrophobic	false
O6	ND2	ASN- 194	2.9	171.87	H-Bond (Protein Donor)	false
N1	OD1	ASN- 194	2.58	158.39	H-Bond (Ligand Donor)	false
N2	OD1	ASN- 194	3.24	126.71	H-Bond (Ligand Donor)	false
O2A	O	HOH- 2001	2.64	179.97	H-Bond (Protein Donor)	false
O1B	O	HOH- 2040	2.66	171.71	H-Bond (Protein Donor)	false