0.031162
0.017992
0.000000
0.000000
0.035983
0.000000
0.000000
0.000000
0.006657
0.00000
0.00000
0.00000
Ponna, S.K.
Myllykoski, M.
Boeckers, T.M.
Kursula, P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
32.090
32.090
150.220
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
J. Neurochem.
1471-4159
145
449
463
10.1111/jnc.14322
29473168
Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3.
2018
100
1
PIXEL
2016-05-28
DECTRIS PILATUS3 6M
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
P13 (MX1)
PETRA III, EMBL c/o DESY
1.000
SYNCHROTRON
PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
10400.004
SH3 and multiple ankyrin repeat domains protein 3
PDZ domain, UNP residues 570-664
1
man
polymer
685.810
Adhesion G protein-coupled receptor L1
UNP residues 1510-1515
1
syn
polymer
18.015
water
63
nat
water
Shank3,Proline-rich synapse-associated protein 2,ProSAP2,SPANK-2
Calcium-independent alpha-latrotoxin receptor 1,CIRL-1,Latrophilin-1
no
no
SVAILQKRDHEGFGFVLRGAKAETPIEEFTPTPAFPALQYLESVDVEGVAWKAGLRTGDFLIEVNGVNVVKVGHKQVVGL
IRQGGNRLVMKVVSVT
SVAILQKRDHEGFGFVLRGAKAETPIEEFTPTPAFPALQYLESVDVEGVAWKAGLRTGDFLIEVNGVNVVKVGHKQVVGL
IRQGGNRLVMKVVSVT
A
polypeptide(L)
no
yes
(ACE)QLVTSL
XQLVTSL
B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Rat
sample
1
96
Shank3, Prosap2
10116
Rattus norvegicus
562
Escherichia coli
Biological sequence
1
2.01
38.93
VAPOR DIFFUSION, SITTING DROP
0.1 M HEPES pH 7.5, 2% PEG 400, 2 M ammonium sulphate
293
citation
repository
Initial release
Data collection
Database references
1
0
2018-03-07
1
1
2018-07-11
_citation.journal_volume
_citation.page_first
_citation.page_last
N
PDBE
Y
PDBE
2017-08-29
REL
REL
1
A
O
HOH
755
6.78
HOH
water
10116
Rat
Rattus norvegicus
sample
1
7
HOH
39
3
HOH
HOH
701
A
HOH
64
3
HOH
HOH
702
A
HOH
50
3
HOH
HOH
703
A
HOH
19
3
HOH
HOH
704
A
HOH
28
3
HOH
HOH
705
A
HOH
3
3
HOH
HOH
706
A
HOH
63
3
HOH
HOH
707
A
HOH
4
3
HOH
HOH
708
A
HOH
5
3
HOH
HOH
709
A
HOH
14
3
HOH
HOH
710
A
HOH
27
3
HOH
HOH
711
A
HOH
24
3
HOH
HOH
712
A
HOH
38
3
HOH
HOH
713
A
HOH
33
3
HOH
HOH
714
A
HOH
2
3
HOH
HOH
715
A
HOH
7
3
HOH
HOH
716
A
HOH
37
3
HOH
HOH
717
A
HOH
12
3
HOH
HOH
718
A
HOH
11
3
HOH
HOH
719
A
HOH
17
3
HOH
HOH
720
A
HOH
1
3
HOH
HOH
721
A
HOH
8
3
HOH
HOH
722
A
HOH
16
3
HOH
HOH
723
A
HOH
61
3
HOH
HOH
724
A
HOH
21
3
HOH
HOH
725
A
HOH
52
3
HOH
HOH
726
A
HOH
13
3
HOH
HOH
727
A
HOH
9
3
HOH
HOH
728
A
HOH
40
3
HOH
HOH
729
A
HOH
53
3
HOH
HOH
730
A
HOH
18
3
HOH
HOH
731
A
HOH
32
3
HOH
HOH
732
A
HOH
31
3
HOH
HOH
733
A
HOH
44
3
HOH
HOH
734
A
HOH
20
3
HOH
HOH
735
A
HOH
69
3
HOH
HOH
736
A
HOH
30
3
HOH
HOH
737
A
HOH
36
3
HOH
HOH
738
A
HOH
43
3
HOH
HOH
739
A
HOH
65
3
HOH
HOH
740
A
HOH
29
3
HOH
HOH
741
A
HOH
25
3
HOH
HOH
742
A
HOH
22
3
HOH
HOH
743
A
HOH
67
3
HOH
HOH
744
A
HOH
48
3
HOH
HOH
745
A
HOH
68
3
HOH
HOH
746
A
HOH
23
3
HOH
HOH
747
A
HOH
59
3
HOH
HOH
748
A
HOH
66
3
HOH
HOH
749
A
HOH
26
3
HOH
HOH
750
A
HOH
55
3
HOH
HOH
751
A
HOH
57
3
HOH
HOH
752
A
HOH
60
3
HOH
HOH
753
A
HOH
56
3
HOH
HOH
754
A
HOH
58
3
HOH
HOH
755
A
HOH
15
3
HOH
HOH
1601
B
HOH
6
3
HOH
HOH
1602
B
HOH
45
3
HOH
HOH
1603
B
HOH
35
3
HOH
HOH
1604
B
HOH
10
3
HOH
HOH
1605
B
HOH
42
3
HOH
HOH
1606
B
HOH
54
3
HOH
HOH
1607
B
HOH
62
3
HOH
HOH
1608
B
SER
579
n
1
SER
579
A
VAL
580
n
2
VAL
580
A
ALA
581
n
3
ALA
581
A
ILE
582
n
4
ILE
582
A
LEU
583
n
5
LEU
583
A
GLN
584
n
6
GLN
584
A
LYS
585
n
7
LYS
585
A
ARG
586
n
8
ARG
586
A
ASP
587
n
9
ASP
587
A
HIS
588
n
10
HIS
588
A
GLU
589
n
11
GLU
589
A
GLY
590
n
12
GLY
590
A
PHE
591
n
13
PHE
591
A
GLY
592
n
14
GLY
592
A
PHE
593
n
15
PHE
593
A
VAL
594
n
16
VAL
594
A
LEU
595
n
17
LEU
595
A
ARG
596
n
18
ARG
596
A
GLY
597
n
19
GLY
597
A
ALA
598
n
20
ALA
598
A
LYS
599
n
21
LYS
599
A
ALA
600
n
22
ALA
600
A
GLU
601
n
23
GLU
601
A
THR
602
n
24
THR
602
A
PRO
603
n
25
PRO
603
A
ILE
604
n
26
ILE
604
A
GLU
605
n
27
GLU
605
A
GLU
606
n
28
GLU
606
A
PHE
607
n
29
PHE
607
A
THR
608
n
30
THR
608
A
PRO
609
n
31
PRO
609
A
THR
610
n
32
THR
610
A
PRO
611
n
33
PRO
611
A
ALA
612
n
34
ALA
612
A
PHE
613
n
35
PHE
613
A
PRO
614
n
36
PRO
614
A
ALA
615
n
37
ALA
615
A
LEU
616
n
38
LEU
616
A
GLN
617
n
39
GLN
617
A
TYR
618
n
40
TYR
618
A
LEU
619
n
41
LEU
619
A
GLU
620
n
42
GLU
620
A
SER
621
n
43
SER
621
A
VAL
622
n
44
VAL
622
A
ASP
623
n
45
ASP
623
A
VAL
624
n
46
VAL
624
A
GLU
625
n
47
GLU
625
A
GLY
626
n
48
GLY
626
A
VAL
627
n
49
VAL
627
A
ALA
628
n
50
ALA
628
A
TRP
629
n
51
TRP
629
A
LYS
630
n
52
LYS
630
A
ALA
631
n
53
ALA
631
A
GLY
632
n
54
GLY
632
A
LEU
633
n
55
LEU
633
A
ARG
634
n
56
ARG
634
A
THR
635
n
57
THR
635
A
GLY
636
n
58
GLY
636
A
ASP
637
n
59
ASP
637
A
PHE
638
n
60
PHE
638
A
LEU
639
n
61
LEU
639
A
ILE
640
n
62
ILE
640
A
GLU
641
n
63
GLU
641
A
VAL
642
n
64
VAL
642
A
ASN
643
n
65
ASN
643
A
GLY
644
n
66
GLY
644
A
VAL
645
n
67
VAL
645
A
ASN
646
n
68
ASN
646
A
VAL
647
n
69
VAL
647
A
VAL
648
n
70
VAL
648
A
LYS
649
n
71
LYS
649
A
VAL
650
n
72
VAL
650
A
GLY
651
n
73
GLY
651
A
HIS
652
n
74
HIS
652
A
LYS
653
n
75
LYS
653
A
GLN
654
n
76
GLN
654
A
VAL
655
n
77
VAL
655
A
VAL
656
n
78
VAL
656
A
GLY
657
n
79
GLY
657
A
LEU
658
n
80
LEU
658
A
ILE
659
n
81
ILE
659
A
ARG
660
n
82
ARG
660
A
GLN
661
n
83
GLN
661
A
GLY
662
n
84
GLY
662
A
GLY
663
n
85
GLY
663
A
ASN
664
n
86
ASN
664
A
ARG
665
n
87
ARG
665
A
LEU
666
n
88
LEU
666
A
VAL
667
n
89
VAL
667
A
MET
668
n
90
MET
668
A
LYS
669
n
91
LYS
669
A
VAL
670
n
92
VAL
670
A
VAL
671
n
93
VAL
671
A
SER
672
n
94
SER
672
A
VAL
673
n
95
VAL
673
A
THR
674
n
96
THR
674
A
ACE
1509
n
1
ACE
1509
B
GLN
1510
n
2
GLN
1510
B
LEU
1511
n
3
LEU
1511
B
VAL
1512
n
4
VAL
1512
B
THR
1513
n
5
THR
1513
B
SER
1514
n
6
SER
1514
B
LEU
1515
n
7
LEU
1515
B
1.1456
-0.6894
-0.2063
0.5420
-0.1597
1.5710
-0.0885
-0.0893
0.0724
0.1139
0.1514
-0.0047
0.1484
0.1763
0.0008
0.1754
0.0067
-0.0070
0.1746
-0.0190
0.1726
refined
-8.3068
-6.0155
14.1081
X-RAY DIFFRACTION
0.0338
-0.1690
0.0072
-0.0087
-0.0534
0.0071
0.1952
-0.0323
-0.0677
-0.0011
-0.0860
-0.0698
-0.3088
0.2008
0.0001
0.2160
0.0376
0.0043
0.2755
0.0188
0.2192
refined
-5.9267
-6.2636
19.0146
X-RAY DIFFRACTION
0.0674
0.0565
-0.0307
0.0516
-0.0575
0.0549
0.1689
0.0095
0.1603
-0.1543
0.0427
-0.3616
-0.1299
-0.1483
-0.0001
0.2344
0.0150
-0.0138
0.2057
-0.0065
0.1642
refined
-12.2920
-5.2760
5.0030
X-RAY DIFFRACTION
1.0680
0.1225
-0.1888
0.3514
-0.8195
1.1255
0.0533
-0.0723
0.0883
-0.0757
0.1969
-0.0764
-0.0660
-0.1497
0.1426
0.2242
0.0668
-0.0280
0.1710
0.0071
0.1471
refined
-11.3504
-6.8600
13.3467
X-RAY DIFFRACTION
0.4824
-0.0264
-0.7335
0.4549
0.0058
1.1226
-0.3147
0.3004
-0.2938
-0.5687
0.3565
-0.2559
0.3041
0.0896
-0.0059
0.2744
0.1934
0.1067
0.1908
-0.0556
0.2794
refined
0.4230
-17.0586
9.3722
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
chain 'A' and (resid 617 through 662 )
X-RAY DIFFRACTION
2
chain 'A' and (resid 663 through 674 )
X-RAY DIFFRACTION
3
chain 'B' and (resid 1510 through 1515 )
X-RAY DIFFRACTION
4
chain 'A' and (resid 579 through 607 )
X-RAY DIFFRACTION
5
chain 'A' and (resid 608 through 616 )
author_and_software_defined_assembly
PISA
2
dimeric
SAXS
1140
-5
5630
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
583
A
N
LEU
5
A
O
LEU
666
A
O
LEU
88
A
O
VAL
671
A
O
VAL
93
A
N
PHE
638
A
N
PHE
60
A
N
VAL
642
A
N
VAL
64
A
O
VAL
645
A
O
VAL
67
A
O
TYR
618
A
O
TYR
40
A
N
ARG
596
A
N
ARG
18
A
N
GLY
597
A
N
GLY
19
B
O
LEU
1511
B
O
LEU
3
1
A
HOH
749
C
HOH
1
A
HOH
751
C
HOH
1
A
B
O
O
HOH
HOH
731
1606
2.17
1
B
B
O
O
HOH
HOH
1607
1608
1.90
1_555
6_555
1
A
ALA
600
-162.83
-39.28
1
A
GLU
601
70.09
-45.26
1
A
GLU
605
-170.97
-69.28
0.2355
0.1934
0.1954
1.500
27.791
737
14613
5.04
99.61
0.21
1
FREE R-VALUE
1.36
30.91
0.90
1.11
1.500
27.791
63
846
0
0
783
0.011
813
1.038
1104
21.263
299
0.085
131
0.008
143
0.3763
0.3365
1.6158
144
2728
99.00
0.2782
0.2648
1.7784
149
2733
100.00
0.2471
0.2011
2.0356
146
2739
100.00
0.2319
0.1920
2.5644
147
2781
100.00
0.2150
0.1702
27.7955
151
2895
100.00
28
1.50
50
5OVP
14688
1.00
0.095
1
15.4
10.7
99.7
1.50
1.54
1055
0.557
2.457
1
10
98.4
refinement
PHENIX
(1.11.1_2575: ???)
data reduction
XDS
data scaling
XDS
phasing
PHASER
N
SH3 and multiple ankyrin repeat domains protein 3, Adhesion G protein-coupled receptor L1
PDZ domain from rat Shank3 bound to the C terminus of CIRL
1
N
N
2
N
N
3
N
N
3
N
N
A
GLY
626
A
GLY
48
HELX_P
A
ALA
631
A
ALA
53
1
AA1
6
A
GLY
651
A
GLY
73
HELX_P
A
GLY
662
A
GLY
84
1
AA2
12
covale
1.317
both
B
ACE
1509
B
C
ACE
1
1_555
B
GLN
1510
B
N
GLN
2
1_555
PROTEIN BINDING
PDZ domain, peptide binding, post-synaptic density, C terminus, PROTEIN BINDING
A
ILE
604
A
ILE
26
1
A
GLU
605
A
GLU
27
5.85
SHAN3_RAT
UNP
1
570
Q9JLU4
VAILQKRDHEGFGFVLRGAKAETPIEEFTPTPAFPALQYLESVDVEGVAWKAGLRTGDFLIEVNGVNVVKVGHKQVVGLI
RQGGNRLVMKVVSVT
AGRL1_RAT
UNP
2
1510
O88917
QLVTSL
570
664
5OVP
580
674
Q9JLU4
A
1
2
96
1510
1515
5OVP
1510
1515
O88917
B
2
2
7
1
expression tag
SER
579
5OVP
A
Q9JLU4
UNP
1
2
acetylation
ACE
1509
5OVP
B
O88917
UNP
1
4
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
580
A
VAL
2
A
GLN
584
A
GLN
6
A
ARG
665
A
ARG
87
A
SER
672
A
SER
94
A
ASP
637
A
ASP
59
A
VAL
642
A
VAL
64
A
VAL
645
A
VAL
67
A
ASN
646
A
ASN
68
A
GLN
617
A
GLN
39
A
VAL
622
A
VAL
44
A
PHE
593
A
PHE
15
A
GLY
597
A
GLY
19
B
LEU
1511
B
LEU
3
B
SER
1514
B
SER
6
153
P 32 1 2