scPDB - 3daf entry

Protein Data Bank Entry:

PDB ID : 3daf

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2008-05-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5,10-methenyltetrahydromethanopterin hydrogenase
ID:	HMD_METJA
AC:	Q58194
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	1.12.98.2

Chains:

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

Ligand binding site composition:

B-Factor:	31.176
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.084	502.875

% Hydrophobic	% Polar
55.70	44.30
According to VolSite

Ligand :

HET Code:	FEG
Formula:	C19H21N6O11P
Molecular weight:	540.377 g/mol
DrugBank ID:	-
Buried Surface Area:	64.13 %
Polar Surface area:	276.64 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
23.1701	9.40665	31.7215

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
O3S	N	GLY- 9	2.83	134.07	H-Bond (Protein Donor)	false
O2P	N	CYS- 10	3.13	157.06	H-Bond (Protein Donor)	false
O18	OG1	THR- 13	3.09	159.34	H-Bond (Protein Donor)	false
N2A	O	SER- 63	3	128.71	H-Bond (Ligand Donor)	false
O3S	OD2	ASP- 64	2.61	145.43	H-Bond (Ligand Donor)	false
O2S	OD2	ASP- 64	3.16	156.27	H-Bond (Ligand Donor)	false
O2S	OD1	ASP- 64	2.67	134.98	H-Bond (Ligand Donor)	false
C2S	CB	PRO- 114	3.69	0	Hydrophobic	false
C2S	CB	PRO- 115	4.26	0	Hydrophobic	false
C3S	SG	CYS- 118	4.13	0	Hydrophobic	false
N1A	OD2	ASP- 135	2.91	169.56	H-Bond (Ligand Donor)	false
N2A	OD1	ASP- 135	2.83	145.25	H-Bond (Ligand Donor)	false
N2A	OD2	ASP- 135	3.48	134.87	H-Bond (Ligand Donor)	false
C3M	CE2	TRP- 148	3.57	0	Hydrophobic	false
C1S	CG	PRO- 150	3.95	0	Hydrophobic	false
C4S	CG	PRO- 150	4.32	0	Hydrophobic	false
C7	SG	CYS- 176	4.39	0	Hydrophobic	false
C3M	CG2	THR- 177	3.84	0	Hydrophobic	false
O2P	O	HOH- 2067	2.55	179.98	H-Bond (Protein Donor)	false