Fluorine in PDB 5j3j: Crystal Structure of Human Dpp-IV in Complex with HL1
Enzymatic activity of Crystal Structure of Human Dpp-IV in Complex with HL1
All present enzymatic activity of Crystal Structure of Human Dpp-IV in Complex with HL1:
3.4.14.5;
Protein crystallography data
The structure of Crystal Structure of Human Dpp-IV in Complex with HL1, PDB code: 5j3j
was solved by
F.Wu,
H.Li,
Z.Zhao,
L.Zhu,
H.Xu,
S.Li,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
55.11 /
2.75
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.360,
126.820,
112.620,
90.00,
99.95,
90.00
|
R / Rfree (%)
|
23.5 /
29.8
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Human Dpp-IV in Complex with HL1
(pdb code 5j3j). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of Human Dpp-IV in Complex with HL1, PDB code: 5j3j:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 5j3j
Go back to
Fluorine Binding Sites List in 5j3j
Fluorine binding site 1 out
of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Human Dpp-IV in Complex with HL1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:25.7
occ:1.00
|
F7
|
A:HL1801
|
0.0
|
25.7
|
1.0
|
C1
|
A:HL1801
|
1.3
|
25.6
|
1.0
|
C6
|
A:HL1801
|
2.4
|
25.6
|
1.0
|
C2
|
A:HL1801
|
2.4
|
25.2
|
1.0
|
C10
|
A:HL1801
|
2.8
|
24.5
|
1.0
|
ND2
|
A:ASN710
|
2.9
|
19.8
|
1.0
|
NH2
|
A:ARG125
|
3.3
|
20.2
|
1.0
|
OE2
|
A:GLU205
|
3.3
|
19.2
|
1.0
|
OH
|
A:TYR662
|
3.3
|
20.6
|
1.0
|
N16
|
A:HL1801
|
3.3
|
23.9
|
1.0
|
C5
|
A:HL1801
|
3.6
|
25.9
|
1.0
|
CG
|
A:ASN710
|
3.6
|
19.8
|
1.0
|
C3
|
A:HL1801
|
3.6
|
25.6
|
1.0
|
C15
|
A:HL1801
|
3.7
|
24.0
|
1.0
|
NE2
|
A:HIS740
|
3.7
|
26.6
|
1.0
|
CD2
|
A:HIS740
|
3.8
|
26.3
|
1.0
|
OD1
|
A:ASN710
|
3.9
|
20.0
|
1.0
|
O11
|
A:HL1801
|
4.0
|
24.4
|
1.0
|
C4
|
A:HL1801
|
4.1
|
25.9
|
1.0
|
OG
|
A:SER630
|
4.2
|
23.2
|
1.0
|
CD
|
A:GLU205
|
4.4
|
19.4
|
1.0
|
CZ
|
A:TYR662
|
4.5
|
20.7
|
1.0
|
CZ
|
A:ARG125
|
4.6
|
20.2
|
1.0
|
CE1
|
A:HIS740
|
4.6
|
26.5
|
1.0
|
C14
|
A:HL1801
|
4.7
|
23.9
|
1.0
|
F8
|
A:HL1801
|
4.7
|
26.9
|
1.0
|
CG
|
A:HIS740
|
4.8
|
26.0
|
1.0
|
CB
|
A:ASN710
|
4.8
|
19.7
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 5j3j
Go back to
Fluorine Binding Sites List in 5j3j
Fluorine binding site 2 out
of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Human Dpp-IV in Complex with HL1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:26.9
occ:1.00
|
F8
|
A:HL1801
|
0.0
|
26.9
|
1.0
|
C5
|
A:HL1801
|
1.3
|
25.9
|
1.0
|
C6
|
A:HL1801
|
2.4
|
25.6
|
1.0
|
C4
|
A:HL1801
|
2.4
|
25.9
|
1.0
|
F9
|
A:HL1801
|
2.8
|
25.1
|
1.0
|
CG2
|
A:VAL711
|
3.1
|
19.3
|
1.0
|
CG2
|
A:VAL656
|
3.2
|
17.7
|
1.0
|
OG
|
A:SER630
|
3.3
|
23.2
|
1.0
|
C3
|
A:HL1801
|
3.6
|
25.6
|
1.0
|
C1
|
A:HL1801
|
3.6
|
25.6
|
1.0
|
N
|
A:TYR631
|
3.7
|
21.3
|
1.0
|
C
|
A:SER630
|
3.8
|
22.3
|
1.0
|
C2
|
A:HL1801
|
4.1
|
25.2
|
1.0
|
CA
|
A:SER630
|
4.1
|
22.6
|
1.0
|
CE1
|
A:TYR662
|
4.2
|
20.6
|
1.0
|
CB
|
A:SER630
|
4.2
|
22.9
|
1.0
|
CZ
|
A:TYR662
|
4.3
|
20.7
|
1.0
|
O
|
A:SER630
|
4.3
|
23.0
|
1.0
|
CB
|
A:VAL656
|
4.3
|
17.9
|
1.0
|
CA
|
A:TYR631
|
4.4
|
20.6
|
1.0
|
CE1
|
A:HIS740
|
4.4
|
26.5
|
1.0
|
OH
|
A:TYR662
|
4.4
|
20.6
|
1.0
|
NE2
|
A:HIS740
|
4.5
|
26.6
|
1.0
|
CB
|
A:VAL711
|
4.5
|
19.2
|
1.0
|
CD1
|
A:TYR662
|
4.6
|
20.4
|
1.0
|
F7
|
A:HL1801
|
4.7
|
25.7
|
1.0
|
N
|
A:VAL656
|
4.8
|
17.6
|
1.0
|
CB
|
A:TYR631
|
4.8
|
20.5
|
1.0
|
O
|
A:ALA654
|
4.8
|
18.4
|
1.0
|
CE2
|
A:TYR662
|
4.9
|
20.4
|
1.0
|
CG1
|
A:VAL711
|
4.9
|
19.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 5j3j
Go back to
Fluorine Binding Sites List in 5j3j
Fluorine binding site 3 out
of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Human Dpp-IV in Complex with HL1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F801
b:25.1
occ:1.00
|
F9
|
A:HL1801
|
0.0
|
25.1
|
1.0
|
C4
|
A:HL1801
|
1.3
|
25.9
|
1.0
|
C3
|
A:HL1801
|
2.4
|
25.6
|
1.0
|
C5
|
A:HL1801
|
2.4
|
25.9
|
1.0
|
F8
|
A:HL1801
|
2.8
|
26.9
|
1.0
|
CD2
|
A:TYR631
|
3.1
|
19.7
|
1.0
|
CB
|
A:TYR631
|
3.5
|
20.5
|
1.0
|
OH
|
A:TYR666
|
3.5
|
15.4
|
1.0
|
C2
|
A:HL1801
|
3.6
|
25.2
|
1.0
|
C6
|
A:HL1801
|
3.6
|
25.6
|
1.0
|
CZ
|
A:TYR666
|
3.7
|
15.7
|
1.0
|
CG
|
A:TYR631
|
3.8
|
19.9
|
1.0
|
CE1
|
A:TYR666
|
3.8
|
15.7
|
1.0
|
CA
|
A:TYR631
|
3.9
|
20.6
|
1.0
|
N
|
A:TYR631
|
4.0
|
21.3
|
1.0
|
C1
|
A:HL1801
|
4.1
|
25.6
|
1.0
|
CE2
|
A:TYR631
|
4.2
|
19.4
|
1.0
|
CH2
|
A:TRP659
|
4.3
|
18.9
|
1.0
|
OG
|
A:SER630
|
4.4
|
23.2
|
1.0
|
CZ3
|
A:TRP659
|
4.5
|
18.9
|
1.0
|
OH
|
A:TYR547
|
4.5
|
27.7
|
1.0
|
CE2
|
A:TYR666
|
4.5
|
15.7
|
1.0
|
CG2
|
A:VAL656
|
4.6
|
17.7
|
1.0
|
CD1
|
A:TYR666
|
4.6
|
15.8
|
1.0
|
CE2
|
A:TYR662
|
4.7
|
20.4
|
1.0
|
CZ
|
A:TYR662
|
4.8
|
20.7
|
1.0
|
C10
|
A:HL1801
|
4.9
|
24.5
|
1.0
|
C
|
A:SER630
|
4.9
|
22.3
|
1.0
|
O11
|
A:HL1801
|
4.9
|
24.4
|
1.0
|
OH
|
A:TYR662
|
5.0
|
20.6
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 5j3j
Go back to
Fluorine Binding Sites List in 5j3j
Fluorine binding site 4 out
of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Human Dpp-IV in Complex with HL1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:18.7
occ:1.00
|
F7
|
B:HL1801
|
0.0
|
18.7
|
1.0
|
C1
|
B:HL1801
|
1.3
|
18.6
|
1.0
|
C6
|
B:HL1801
|
2.4
|
18.6
|
1.0
|
C2
|
B:HL1801
|
2.4
|
18.5
|
1.0
|
C10
|
B:HL1801
|
2.9
|
18.3
|
1.0
|
ND2
|
B:ASN710
|
2.9
|
17.6
|
1.0
|
NH2
|
B:ARG125
|
3.1
|
22.1
|
1.0
|
N16
|
B:HL1801
|
3.3
|
18.4
|
1.0
|
OE2
|
B:GLU205
|
3.3
|
17.0
|
1.0
|
OH
|
B:TYR662
|
3.5
|
18.5
|
1.0
|
CG
|
B:ASN710
|
3.6
|
17.4
|
1.0
|
C5
|
B:HL1801
|
3.6
|
18.6
|
1.0
|
C3
|
B:HL1801
|
3.6
|
18.4
|
1.0
|
C15
|
B:HL1801
|
3.7
|
18.3
|
1.0
|
OD1
|
B:ASN710
|
3.7
|
17.6
|
1.0
|
O
|
B:HOH902
|
3.8
|
32.6
|
1.0
|
CD2
|
B:HIS740
|
4.0
|
19.5
|
1.0
|
O11
|
B:HL1801
|
4.1
|
18.4
|
1.0
|
NE2
|
B:HIS740
|
4.1
|
19.6
|
1.0
|
C4
|
B:HL1801
|
4.1
|
18.4
|
1.0
|
OG
|
B:SER630
|
4.3
|
18.3
|
1.0
|
CZ
|
B:ARG125
|
4.3
|
22.4
|
1.0
|
CD
|
B:GLU205
|
4.5
|
17.4
|
1.0
|
C14
|
B:HL1801
|
4.7
|
18.5
|
1.0
|
CZ
|
B:TYR662
|
4.7
|
18.6
|
1.0
|
F8
|
B:HL1801
|
4.8
|
18.5
|
1.0
|
CB
|
B:ASN710
|
4.8
|
17.4
|
1.0
|
CG
|
B:HIS740
|
5.0
|
19.3
|
1.0
|
CE1
|
B:HIS740
|
5.0
|
19.6
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 5j3j
Go back to
Fluorine Binding Sites List in 5j3j
Fluorine binding site 5 out
of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Human Dpp-IV in Complex with HL1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:18.5
occ:1.00
|
F8
|
B:HL1801
|
0.0
|
18.5
|
1.0
|
C5
|
B:HL1801
|
1.3
|
18.6
|
1.0
|
C4
|
B:HL1801
|
2.4
|
18.4
|
1.0
|
C6
|
B:HL1801
|
2.4
|
18.6
|
1.0
|
F9
|
B:HL1801
|
2.7
|
18.4
|
1.0
|
CG2
|
B:VAL711
|
3.1
|
18.1
|
1.0
|
OG
|
B:SER630
|
3.1
|
18.3
|
1.0
|
CG2
|
B:VAL656
|
3.2
|
17.1
|
1.0
|
C3
|
B:HL1801
|
3.6
|
18.4
|
1.0
|
C1
|
B:HL1801
|
3.7
|
18.6
|
1.0
|
N
|
B:TYR631
|
3.9
|
18.2
|
1.0
|
CE1
|
B:TYR662
|
4.0
|
18.4
|
1.0
|
CZ
|
B:TYR662
|
4.1
|
18.6
|
1.0
|
C2
|
B:HL1801
|
4.1
|
18.5
|
1.0
|
C
|
B:SER630
|
4.2
|
18.1
|
1.0
|
CB
|
B:SER630
|
4.3
|
18.4
|
1.0
|
OH
|
B:TYR662
|
4.3
|
18.5
|
1.0
|
CA
|
B:SER630
|
4.3
|
18.4
|
1.0
|
CB
|
B:VAL711
|
4.4
|
17.9
|
1.0
|
CD1
|
B:TYR662
|
4.4
|
18.5
|
1.0
|
CA
|
B:TYR631
|
4.6
|
18.2
|
1.0
|
CB
|
B:VAL656
|
4.6
|
17.1
|
1.0
|
CE1
|
B:HIS740
|
4.6
|
19.6
|
1.0
|
CE2
|
B:TYR662
|
4.7
|
18.7
|
1.0
|
NE2
|
B:HIS740
|
4.7
|
19.6
|
1.0
|
CG1
|
B:VAL711
|
4.7
|
17.9
|
1.0
|
F7
|
B:HL1801
|
4.8
|
18.7
|
1.0
|
O
|
B:SER630
|
4.8
|
18.0
|
1.0
|
CB
|
B:TYR631
|
4.9
|
18.4
|
1.0
|
CG
|
B:TYR662
|
5.0
|
18.8
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 5j3j
Go back to
Fluorine Binding Sites List in 5j3j
Fluorine binding site 6 out
of 6 in the Crystal Structure of Human Dpp-IV in Complex with HL1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Human Dpp-IV in Complex with HL1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F801
b:18.4
occ:1.00
|
F9
|
B:HL1801
|
0.0
|
18.4
|
1.0
|
C4
|
B:HL1801
|
1.3
|
18.4
|
1.0
|
C5
|
B:HL1801
|
2.4
|
18.6
|
1.0
|
C3
|
B:HL1801
|
2.4
|
18.4
|
1.0
|
F8
|
B:HL1801
|
2.7
|
18.5
|
1.0
|
CD2
|
B:TYR631
|
3.3
|
18.4
|
1.0
|
CE2
|
B:TYR666
|
3.5
|
17.7
|
1.0
|
OH
|
B:TYR666
|
3.6
|
17.6
|
1.0
|
CZ
|
B:TYR666
|
3.6
|
17.8
|
1.0
|
C6
|
B:HL1801
|
3.6
|
18.6
|
1.0
|
C2
|
B:HL1801
|
3.6
|
18.5
|
1.0
|
CB
|
B:TYR631
|
3.7
|
18.4
|
1.0
|
CG
|
B:TYR631
|
4.0
|
18.5
|
1.0
|
C1
|
B:HL1801
|
4.1
|
18.6
|
1.0
|
CH2
|
B:TRP659
|
4.1
|
18.5
|
1.0
|
CD2
|
B:TYR666
|
4.2
|
17.7
|
1.0
|
CA
|
B:TYR631
|
4.2
|
18.2
|
1.0
|
N
|
B:TYR631
|
4.3
|
18.2
|
1.0
|
CE2
|
B:TYR631
|
4.3
|
18.4
|
1.0
|
CE2
|
B:TYR662
|
4.4
|
18.7
|
1.0
|
OG
|
B:SER630
|
4.5
|
18.3
|
1.0
|
CG2
|
B:VAL656
|
4.5
|
17.1
|
1.0
|
CE1
|
B:TYR666
|
4.5
|
17.9
|
1.0
|
CZ3
|
B:TRP659
|
4.5
|
18.6
|
1.0
|
CZ
|
B:TYR662
|
4.5
|
18.6
|
1.0
|
OH
|
B:TYR662
|
4.7
|
18.5
|
1.0
|
C10
|
B:HL1801
|
4.8
|
18.3
|
1.0
|
CD2
|
B:TYR662
|
4.9
|
18.9
|
1.0
|
O11
|
B:HL1801
|
4.9
|
18.4
|
1.0
|
|
Reference:
F.Wu,
H.Li,
Z.Zhao,
L.Zhu,
H.Xu,
S.Li.
Crystal Structure of Human Dpp-IV in Complex with HL1 To Be Published.
Page generated: Thu Aug 1 10:23:55 2024
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