0.014077
0.008127
0.000000
0.000000
0.016254
0.000000
0.000000
0.000000
0.019084
0.00000
0.00000
0.00000
Trillo-Muyo, S.
Martinez-Rodriguez, S.
Arolas, J.L.
Gomis-Ruth, F.X.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
71.040
71.040
52.400
C2 H3 O2 -1
59.044
ACETATE ION
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
C3 H7 N O2 S
121.158
y
CYSTEINE
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
CHEM SCI
2041-6520
4
791
797
10.1039/C2SC21712K
Mechanism of action of a Janus-faced single-domain protein inhibitor simultaneously targeting two peptidase classes
2013
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2009-10-06
MARMOSAIC 225 mm CCD
Si(311)
SINGLE WAVELENGTH
M
x-ray
1
0.8726
1.0
ID23-2
ESRF
0.8726
SYNCHROTRON
ESRF BEAMLINE ID23-2
11923.354
Neutral proteinase inhibitor ScNPI
1
man
polymer
92.094
GLYCEROL
1
syn
non-polymer
59.044
ACETATE ION
3
syn
non-polymer
18.015
water
126
nat
water
Sermetstatin
no
no
GSAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVT
ADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF
GSAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVT
ADGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF
A
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
n
n
n
n
n
n
n
n
n
n
n
sample
ScNPI
53502
Streptomyces caespitosus
562
Escherichia coli
Origami
pET
pET32a
1
3.20
61.58
VAPOR DIFFUSION, SITTING DROP
5.6
0.1 M sodium citrate dihydrate, 0.2 M ammonium acetate, 10% (w/v) PEG3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
software
repository
Initial release
Database references
Refinement description
1
0
2012-12-05
1
1
2013-02-20
1
2
2017-11-15
_software.name
RCSB
Y
RCSB
2012-11-09
REL
REL
GOL
GLYCEROL
ACT
ACETATE ION
HOH
water
GOL
501
2
GOL
GOL
501
A
ACT
502
3
ACT
ACT
502
A
ACT
503
3
ACT
ACT
503
A
ACT
504
3
ACT
ACT
504
A
HOH
505
4
HOH
HOH
601
A
HOH
506
4
HOH
HOH
602
A
HOH
507
4
HOH
HOH
603
A
HOH
508
4
HOH
HOH
604
A
HOH
509
4
HOH
HOH
605
A
HOH
510
4
HOH
HOH
606
A
HOH
511
4
HOH
HOH
607
A
HOH
512
4
HOH
HOH
608
A
HOH
513
4
HOH
HOH
609
A
HOH
514
4
HOH
HOH
610
A
HOH
515
4
HOH
HOH
611
A
HOH
516
4
HOH
HOH
612
A
HOH
517
4
HOH
HOH
613
A
HOH
518
4
HOH
HOH
614
A
HOH
519
4
HOH
HOH
615
A
HOH
520
4
HOH
HOH
616
A
HOH
521
4
HOH
HOH
617
A
HOH
522
4
HOH
HOH
618
A
HOH
523
4
HOH
HOH
619
A
HOH
524
4
HOH
HOH
620
A
HOH
525
4
HOH
HOH
621
A
HOH
526
4
HOH
HOH
622
A
HOH
527
4
HOH
HOH
623
A
HOH
528
4
HOH
HOH
624
A
HOH
529
4
HOH
HOH
625
A
HOH
530
4
HOH
HOH
626
A
HOH
531
4
HOH
HOH
627
A
HOH
532
4
HOH
HOH
628
A
HOH
533
4
HOH
HOH
629
A
HOH
534
4
HOH
HOH
630
A
HOH
535
4
HOH
HOH
631
A
HOH
536
4
HOH
HOH
632
A
HOH
537
4
HOH
HOH
633
A
HOH
538
4
HOH
HOH
634
A
HOH
539
4
HOH
HOH
635
A
HOH
540
4
HOH
HOH
636
A
HOH
541
4
HOH
HOH
637
A
HOH
542
4
HOH
HOH
638
A
HOH
543
4
HOH
HOH
639
A
HOH
544
4
HOH
HOH
640
A
HOH
545
4
HOH
HOH
641
A
HOH
546
4
HOH
HOH
642
A
HOH
547
4
HOH
HOH
643
A
HOH
548
4
HOH
HOH
644
A
HOH
549
4
HOH
HOH
645
A
HOH
550
4
HOH
HOH
646
A
HOH
551
4
HOH
HOH
647
A
HOH
552
4
HOH
HOH
648
A
HOH
553
4
HOH
HOH
649
A
HOH
554
4
HOH
HOH
650
A
HOH
555
4
HOH
HOH
651
A
HOH
556
4
HOH
HOH
652
A
HOH
557
4
HOH
HOH
653
A
HOH
558
4
HOH
HOH
654
A
HOH
559
4
HOH
HOH
655
A
HOH
560
4
HOH
HOH
656
A
HOH
561
4
HOH
HOH
657
A
HOH
562
4
HOH
HOH
658
A
HOH
563
4
HOH
HOH
659
A
HOH
564
4
HOH
HOH
660
A
HOH
565
4
HOH
HOH
661
A
HOH
566
4
HOH
HOH
662
A
HOH
567
4
HOH
HOH
663
A
HOH
568
4
HOH
HOH
664
A
HOH
569
4
HOH
HOH
665
A
HOH
570
4
HOH
HOH
666
A
HOH
571
4
HOH
HOH
667
A
HOH
572
4
HOH
HOH
668
A
HOH
573
4
HOH
HOH
669
A
HOH
574
4
HOH
HOH
670
A
HOH
575
4
HOH
HOH
671
A
HOH
576
4
HOH
HOH
672
A
HOH
577
4
HOH
HOH
673
A
HOH
578
4
HOH
HOH
674
A
HOH
579
4
HOH
HOH
675
A
HOH
580
4
HOH
HOH
676
A
HOH
581
4
HOH
HOH
677
A
HOH
582
4
HOH
HOH
678
A
HOH
583
4
HOH
HOH
679
A
HOH
584
4
HOH
HOH
680
A
HOH
585
4
HOH
HOH
681
A
HOH
586
4
HOH
HOH
682
A
HOH
587
4
HOH
HOH
683
A
HOH
588
4
HOH
HOH
684
A
HOH
589
4
HOH
HOH
685
A
HOH
590
4
HOH
HOH
686
A
HOH
591
4
HOH
HOH
687
A
HOH
592
4
HOH
HOH
688
A
HOH
593
4
HOH
HOH
689
A
HOH
594
4
HOH
HOH
690
A
HOH
595
4
HOH
HOH
691
A
HOH
596
4
HOH
HOH
692
A
HOH
597
4
HOH
HOH
693
A
HOH
598
4
HOH
HOH
694
A
HOH
599
4
HOH
HOH
695
A
HOH
600
4
HOH
HOH
696
A
HOH
601
4
HOH
HOH
697
A
HOH
602
4
HOH
HOH
698
A
HOH
603
4
HOH
HOH
699
A
HOH
604
4
HOH
HOH
700
A
HOH
605
4
HOH
HOH
701
A
HOH
606
4
HOH
HOH
702
A
HOH
607
4
HOH
HOH
703
A
HOH
608
4
HOH
HOH
704
A
HOH
609
4
HOH
HOH
705
A
HOH
610
4
HOH
HOH
706
A
HOH
611
4
HOH
HOH
707
A
HOH
612
4
HOH
HOH
708
A
HOH
613
4
HOH
HOH
709
A
HOH
614
4
HOH
HOH
710
A
HOH
615
4
HOH
HOH
711
A
HOH
616
4
HOH
HOH
712
A
HOH
617
4
HOH
HOH
713
A
HOH
618
4
HOH
HOH
714
A
HOH
619
4
HOH
HOH
715
A
HOH
620
4
HOH
HOH
716
A
HOH
621
4
HOH
HOH
717
A
HOH
622
4
HOH
HOH
718
A
HOH
623
4
HOH
HOH
719
A
HOH
624
4
HOH
HOH
720
A
HOH
625
4
HOH
HOH
721
A
HOH
626
4
HOH
HOH
722
A
HOH
627
4
HOH
HOH
723
A
HOH
628
4
HOH
HOH
724
A
HOH
629
4
HOH
HOH
725
A
HOH
630
4
HOH
HOH
726
A
GLY
-1
n
1
GLY
-1
A
SER
1
n
2
SER
1
A
ALA
2
n
3
ALA
2
A
HIS
3
n
4
HIS
3
A
GLY
4
n
5
GLY
4
A
PRO
5
n
6
PRO
5
A
SER
6
n
7
SER
6
A
ALA
7
n
8
ALA
7
A
MET
8
n
9
MET
8
A
VAL
9
n
10
VAL
9
A
PHE
10
n
11
PHE
10
A
THR
11
n
12
THR
11
A
VAL
12
n
13
VAL
12
A
ILE
13
n
14
ILE
13
A
GLN
14
n
15
GLN
14
A
GLY
15
n
16
GLY
15
A
SER
16
n
17
SER
16
A
GLY
17
n
18
GLY
17
A
GLU
18
n
19
GLU
18
A
PRO
19
n
20
PRO
19
A
THR
20
n
21
THR
20
A
ASP
21
n
22
ASP
21
A
THR
22
n
23
THR
22
A
VAL
23
n
24
VAL
23
A
LEU
24
n
25
LEU
24
A
ARG
25
n
26
ARG
25
A
ALA
26
n
27
ALA
26
A
THR
27
n
28
THR
27
A
THR
28
n
29
THR
28
A
LEU
29
n
30
LEU
29
A
SER
30
n
31
SER
30
A
CYS
31
n
32
CYS
31
A
ALA
32
n
33
ALA
32
A
TYR
33
n
34
TYR
33
A
THR
34
n
35
THR
34
A
ALA
35
n
36
ALA
35
A
GLU
36
n
37
GLU
36
A
GLY
37
n
38
GLY
37
A
THR
38
n
39
THR
38
A
HIS
39
n
40
HIS
39
A
PRO
40
n
41
PRO
40
A
ALA
41
n
42
ALA
41
A
PRO
42
n
43
PRO
42
A
ARG
43
n
44
ARG
43
A
ALA
44
n
45
ALA
44
A
ALA
45
n
46
ALA
45
A
CYS
46
n
47
CYS
46
A
ASP
47
n
48
ASP
47
A
ALA
48
n
49
ALA
48
A
LEU
49
n
50
LEU
49
A
ASN
50
n
51
ASN
50
A
ALA
51
n
52
ALA
51
A
THR
52
n
53
THR
52
A
ASP
53
n
54
ASP
53
A
GLY
54
n
55
GLY
54
A
GLU
55
n
56
GLU
55
A
LEU
56
n
57
LEU
56
A
ASN
57
n
58
ASN
57
A
ARG
58
n
59
ARG
58
A
LEU
59
n
60
LEU
59
A
LEU
60
n
61
LEU
60
A
ALA
61
n
62
ALA
61
A
ALA
62
n
63
ALA
62
A
PRO
63
n
64
PRO
63
A
ASP
64
n
65
ASP
64
A
PRO
65
n
66
PRO
65
A
SER
66
n
67
SER
66
A
LEU
67
n
68
LEU
67
A
VAL
68
n
69
VAL
68
A
CYS
69
n
70
CYS
69
A
PRO
70
n
71
PRO
70
A
MET
71
n
72
MET
71
A
TYR
72
n
73
TYR
72
A
PHE
73
n
74
PHE
73
A
ASP
74
n
75
ASP
74
A
PRO
75
n
76
PRO
75
A
VAL
76
n
77
VAL
76
A
THR
77
n
78
THR
77
A
VAL
78
n
79
VAL
78
A
THR
79
n
80
THR
79
A
ALA
80
n
81
ALA
80
A
ASP
81
n
82
ASP
81
A
GLY
82
n
83
GLY
82
A
VAL
83
n
84
VAL
83
A
LEU
84
n
85
LEU
84
A
ASN
85
n
86
ASN
85
A
GLY
86
n
87
GLY
86
A
ARG
87
n
88
ARG
87
A
ARG
88
n
89
ARG
88
A
VAL
89
n
90
VAL
89
A
ALA
90
n
91
ALA
90
A
TRP
91
n
92
TRP
91
A
LYS
92
n
93
LYS
92
A
HIS
93
n
94
HIS
93
A
THR
94
n
95
THR
94
A
PHE
95
n
96
PHE
95
A
SER
96
n
97
SER
96
A
ASN
97
n
98
ASN
97
A
THR
98
n
99
THR
98
A
CYS
99
n
100
CYS
99
A
VAL
100
n
101
VAL
100
A
MET
101
n
102
MET
101
A
SER
102
n
103
SER
102
A
ALA
103
n
104
ALA
103
A
ASN
104
n
105
ASN
104
A
LEU
105
n
106
LEU
105
A
ASN
106
n
107
ASN
106
A
SER
107
n
108
SER
107
A
ASN
108
n
109
ASN
108
A
PRO
109
n
110
PRO
109
A
VAL
110
n
111
VAL
110
A
TYR
111
n
112
TYR
111
A
ALA
112
n
113
ALA
112
A
PHE
113
n
114
PHE
113
A
3.4644
-0.1265
-0.9308
0.0427
0.2121
1.6503
0.1742
0.1376
-0.1384
0.0224
-0.1414
-0.0492
-0.0078
-0.2086
-0.0328
0.0461
-0.0491
-0.0347
0.0134
0.0018
-0.0396
refined
-3.4193
25.3953
2.1786
X-RAY DIFFRACTION
A
-1
A
113
X-RAY DIFFRACTION
1
{ A|* }
author_and_software_defined_assembly
PISA
2
dimeric
software_defined_assembly
PISA
2
dimeric
2970
-17
11790
2310
-18
12440
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
-0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_555
-x,-x+y,-z+1/3
crystal symmetry operation
0.0000000000
0.0000000000
17.4666666667
-0.5000000000
0.8660254038
0.0000000000
0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
O
GLU
36
A
O
GLU
37
A
N
SER
30
A
N
SER
31
A
O
LEU
29
A
O
LEU
30
A
N
MET
8
A
N
MET
9
A
N
ILE
13
A
N
ILE
14
A
O
THR
77
A
O
THR
78
A
N
VAL
76
A
N
VAL
77
A
O
PHE
95
A
O
PHE
96
1
A
ALA
32
-158.10
-137.28
1
A
ASN
106
55.30
-120.78
1
A
SER
107
-140.54
28.41
42.28
-5.4007
0.0000
0.0000
-5.4007
0.0000
10.8015
0.9437
0.9258
0.2140
0.187
0.187
0.1883
1.90
39.89
479
12232
12232
3.92
99.00
0.122
RANDOM
1
THROUGHOUT
0.0
SAD
Engh & Huber
0.273
1.90
39.89
126
978
18
0
834
0.010
870
HARMONIC
2.00
1.14
1191
HARMONIC
2.00
371
SINUSOIDAL
2.00
21
HARMONIC
2.00
131
HARMONIC
5.00
870
HARMONIC
20.00
6
SEMIHARMONIC
5.00
4.01
2.51
119
SEMIHARMONIC
5.00
974
SEMIHARMONIC
4.00
0.2207
0.2167
0.2168
2.08
479
2762
2869
12234
6
3.73
99.00
34.43
1.90
39.9
4HWX
12234
12234
0
0
0.038
1
40.3
99.3
data collection
ProDC
model building
SHELX
& PHASER
refinement
BUSTER
2.11.2
data reduction
XDS
data scaling
SCALA
phasing
SHELX
& PHASER
Neutral proteinase inhibitor ScNPI
Crystal structure of Streptomyces caespitosus sermetstatin
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
4
N
N
A
ALA
41
A
ALA
42
HELX_P
A
THR
52
A
THR
53
1
1
12
A
GLU
55
A
GLU
56
HELX_P
A
LEU
60
A
LEU
61
5
2
6
A
ASN
97
A
ASN
98
HELX_P
A
LEU
105
A
LEU
106
1
3
9
A
ASN
108
A
ASN
109
HELX_P
A
ALA
112
A
ALA
113
5
4
5
disulf
2.034
A
CYS
31
A
SG
CYS
32
1_555
A
CYS
46
A
SG
CYS
47
1_555
disulf
2.050
A
CYS
69
A
SG
CYS
70
1_555
A
CYS
99
A
SG
CYS
100
1_555
Hydrolase Inhibitor
Streptomyces subtilisin inhibitor fold, Hydrolase Inhibitor
Q9FDS0_STRCS
UNP
1
29
Q9FDS0
SAHGPSAMVFTVIQGSGEPTDTVLRATTLSCAYTAEGTHPAPRAACDALNATDGELNRLLAAPDPSLVCPMYFDPVTVTA
DGVLNGRRVAWKHTFSNTCVMSANLNSNPVYAF
29
141
4HWX
1
113
Q9FDS0
A
1
2
114
1
EXPRESSION TAG
GLY
-1
4HWX
A
Q9FDS0
UNP
1
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ALA
35
A
ALA
36
A
GLU
36
A
GLU
37
A
THR
22
A
THR
23
A
CYS
31
A
CYS
32
A
ALA
7
A
ALA
8
A
GLN
14
A
GLN
15
A
VAL
76
A
VAL
77
A
LEU
84
A
LEU
85
A
ARG
87
A
ARG
88
A
PHE
95
A
PHE
96
BINDING SITE FOR RESIDUE GOL A 501
Software
8
BINDING SITE FOR RESIDUE ACT A 502
Software
5
BINDING SITE FOR RESIDUE ACT A 503
Software
3
BINDING SITE FOR RESIDUE ACT A 504
Software
4
A
CYS
31
A
CYS
32
8
1_555
A
ALA
32
A
ALA
33
8
1_555
A
ARG
43
A
ARG
44
8
1_555
A
CYS
46
A
CYS
47
8
1_555
A
ASN
50
A
ASN
51
8
1_555
A
HOH
618
F
HOH
8
1_555
A
HOH
669
F
HOH
8
1_555
A
HOH
670
F
HOH
8
1_555
A
ALA
2
A
ALA
3
5
1_555
A
HIS
3
A
HIS
4
5
1_555
A
SER
66
A
SER
67
5
5_564
A
HOH
669
F
HOH
5
1_555
A
HOH
688
F
HOH
5
1_555
A
ASP
81
A
ASP
82
3
1_555
A
ARG
88
A
ARG
89
3
6_555
A
TRP
91
A
TRP
92
3
1_555
A
LEU
60
A
LEU
61
4
1_555
A
HIS
93
A
HIS
94
4
1_555
A
PHE
95
A
PHE
96
4
1_555
A
HOH
615
F
HOH
4
1_555
152
P 31 2 1