0.009177
0.000000
0.000000
0.000000
0.012358
0.000000
0.000000
0.000000
0.021659
0.00000
0.00000
0.00000
Tabernero, L.
Sack, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
108.970
80.920
46.170
C28 H38 N6 O6
554.638
methyl N-(4-carbamimidamidobutanoyl)-L-phenylalanyl-L-allothreonyl-L-phenylalaninate
BMS-183507
peptide-like
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
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
C9 H11 N O6 S
261.252
n
O-SULFO-L-TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
246
14
20
10.1006/jmbi.1994.0060
7853394
Structure of a retro-binding peptide inhibitor complexed with human alpha-thrombin.
1995
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
x-ray
1
1.0
3791.204
ALPHA-THROMBIN
3.4.21.5
1
nat
polymer
29780.219
ALPHA-THROMBIN
3.4.21.5
1
nat
polymer
1548.580
HIRUGEN PEPTIDE
1
man
polymer
554.638
methyl N-(4-carbamimidamidobutanoyl)-L-phenylalanyl-L-allothreonyl-L-phenylalaninate
1
syn
non-polymer
18.015
water
95
nat
water
no
no
SGEADCGLRPLFEKKSLEDKTERELLESYIDGR
SGEADCGLRPLFEKKSLEDKTERELLESYIDGR
L
polypeptide(L)
no
no
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
H
polypeptide(L)
no
yes
GDFEEIPEE(TYS)LQ
GDFEEIPEEYLQ
P
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
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
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
Medicinal leech
sample
6421
Hirudo medicinalis
human
sample
9606
Homo sapiens
human
sample
9606
Homo sapiens
2.86
56.97
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
1
0
1995-10-15
1
1
2008-03-03
1
2
2011-07-13
1
3
2012-12-12
SHEET
THE SHEETS PRESENTED AS B1 AND B2 ON SHEET RECORDS BELOW
ACTUALLY COMPRISE SIX-STRANDED BETA-BARRELS. THESE ARE
REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND
LAST STRANDS ARE IDENTICAL.
Y
1994-07-25
REL
0E7
methyl N-(4-carbamimidamidobutanoyl)-L-phenylalanyl-L-allothreonyl-L-phenylalaninate
HOH
water
THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN
INDICATOR *L* IS USED FOR RESIDUES 1H - 15. CHAIN
INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN
INDICATOR *P* IS USED FOR THE HIRUGEN PEPTIDE.
THE INHIBITOR IS DESCRIBED AS A FOUR RESIDUE PSEUDO-PEPTIDE CONTAINING AN ALKYL-GUANIDINO GROUP (ALG), TWO PHENYLALANINE GROUPS, AND AN
ALLO-THREONINE (ALO) GROUP.
CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS
USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE
OF CHYMOTRYPSIN (W. BODE ET AL., 1989, EMBO J. 8, 3467 -
3475).
Inhibitor
methyl N-(4-carbamimidamidobutanoyl)-L-phenylalanyl-L-allothreonyl-L-phenylalaninate
Peptide-like
ALG
1
4
0E7
0E7
1
H
HOH
649
5
HOH
HOH
649
L
HOH
650
5
HOH
HOH
650
L
HOH
657
5
HOH
HOH
657
L
HOH
658
5
HOH
HOH
658
L
HOH
683
5
HOH
HOH
683
L
HOH
685
5
HOH
HOH
685
L
HOH
693
5
HOH
HOH
693
L
HOH
601
5
HOH
HOH
601
H
HOH
602
5
HOH
HOH
602
H
HOH
603
5
HOH
HOH
603
H
HOH
605
5
HOH
HOH
605
H
HOH
606
5
HOH
HOH
606
H
HOH
607
5
HOH
HOH
607
H
HOH
608
5
HOH
HOH
608
H
HOH
609
5
HOH
HOH
609
H
HOH
611
5
HOH
HOH
611
H
HOH
612
5
HOH
HOH
612
H
HOH
614
5
HOH
HOH
614
H
HOH
615
5
HOH
HOH
615
H
HOH
616
5
HOH
HOH
616
H
HOH
617
5
HOH
HOH
617
H
HOH
619
5
HOH
HOH
619
H
HOH
620
5
HOH
HOH
620
H
HOH
621
5
HOH
HOH
621
H
HOH
622
5
HOH
HOH
622
H
HOH
623
5
HOH
HOH
623
H
HOH
624
5
HOH
HOH
624
H
HOH
625
5
HOH
HOH
625
H
HOH
627
5
HOH
HOH
627
H
HOH
628
5
HOH
HOH
628
H
HOH
630
5
HOH
HOH
630
H
HOH
631
5
HOH
HOH
631
H
HOH
633
5
HOH
HOH
633
H
HOH
635
5
HOH
HOH
635
H
HOH
636
5
HOH
HOH
636
H
HOH
637
5
HOH
HOH
637
H
HOH
638
5
HOH
HOH
638
H
HOH
639
5
HOH
HOH
639
H
HOH
640
5
HOH
HOH
640
H
HOH
641
5
HOH
HOH
641
H
HOH
642
5
HOH
HOH
642
H
HOH
644
5
HOH
HOH
644
H
HOH
645
5
HOH
HOH
645
H
HOH
646
5
HOH
HOH
646
H
HOH
647
5
HOH
HOH
647
H
HOH
648
5
HOH
HOH
648
H
HOH
651
5
HOH
HOH
651
H
HOH
653
5
HOH
HOH
653
H
HOH
654
5
HOH
HOH
654
H
HOH
655
5
HOH
HOH
655
H
HOH
656
5
HOH
HOH
656
H
HOH
659
5
HOH
HOH
659
H
HOH
664
5
HOH
HOH
664
H
HOH
665
5
HOH
HOH
665
H
HOH
667
5
HOH
HOH
667
H
HOH
668
5
HOH
HOH
668
H
HOH
669
5
HOH
HOH
669
H
HOH
670
5
HOH
HOH
670
H
HOH
673
5
HOH
HOH
673
H
HOH
674
5
HOH
HOH
674
H
HOH
675
5
HOH
HOH
675
H
HOH
676
5
HOH
HOH
676
H
HOH
677
5
HOH
HOH
677
H
HOH
680
5
HOH
HOH
680
H
HOH
681
5
HOH
HOH
681
H
HOH
682
5
HOH
HOH
682
H
HOH
684
5
HOH
HOH
684
H
HOH
686
5
HOH
HOH
686
H
HOH
689
5
HOH
HOH
689
H
HOH
690
5
HOH
HOH
690
H
HOH
692
5
HOH
HOH
692
H
HOH
695
5
HOH
HOH
695
H
HOH
697
5
HOH
HOH
697
H
HOH
698
5
HOH
HOH
698
H
HOH
700
5
HOH
HOH
700
H
HOH
701
5
HOH
HOH
701
H
HOH
702
5
HOH
HOH
702
H
HOH
703
5
HOH
HOH
703
H
HOH
704
5
HOH
HOH
704
H
HOH
705
5
HOH
HOH
705
H
HOH
706
5
HOH
HOH
706
H
HOH
707
5
HOH
HOH
707
H
HOH
709
5
HOH
HOH
709
H
HOH
710
5
HOH
HOH
710
H
HOH
711
5
HOH
HOH
711
H
HOH
712
5
HOH
HOH
712
H
HOH
713
5
HOH
HOH
713
H
HOH
626
5
HOH
HOH
626
P
HOH
634
5
HOH
HOH
634
P
HOH
660
5
HOH
HOH
660
P
HOH
662
5
HOH
HOH
662
P
HOH
672
5
HOH
HOH
672
P
HOH
678
5
HOH
HOH
678
P
HOH
679
5
HOH
HOH
679
P
HOH
688
5
HOH
HOH
688
P
SER
1
n
1
E
SER
1
L
GLY
1
n
2
D
GLY
1
L
GLU
1
n
3
C
GLU
1
L
ALA
1
n
4
B
ALA
1
L
ASP
1
n
5
A
ASP
1
L
CYS
1
n
6
CYS
1
L
GLY
2
n
7
GLY
2
L
LEU
3
n
8
LEU
3
L
ARG
4
n
9
ARG
4
L
PRO
5
n
10
PRO
5
L
LEU
6
n
11
LEU
6
L
PHE
7
n
12
PHE
7
L
GLU
8
n
13
GLU
8
L
LYS
9
n
14
LYS
9
L
LYS
10
n
15
LYS
10
L
SER
11
n
16
SER
11
L
LEU
12
n
17
LEU
12
L
GLU
13
n
18
GLU
13
L
ASP
14
n
19
ASP
14
L
LYS
14
n
20
A
LYS
14
L
THR
14
n
21
B
THR
14
L
GLU
14
n
22
C
GLU
14
L
ARG
14
n
23
D
ARG
14
L
GLU
14
n
24
E
GLU
14
L
LEU
14
n
25
F
LEU
14
L
LEU
14
n
26
G
LEU
14
L
GLU
14
n
27
H
GLU
14
L
SER
14
n
28
I
SER
14
L
TYR
14
n
29
J
TYR
14
L
ILE
14
n
30
K
ILE
14
L
ASP
14
n
31
L
ASP
14
L
GLY
14
n
32
M
GLY
14
L
ARG
15
n
33
ARG
15
L
ILE
16
n
1
ILE
16
H
VAL
17
n
2
VAL
17
H
GLU
18
n
3
GLU
18
H
GLY
19
n
4
GLY
19
H
SER
20
n
5
SER
20
H
ASP
21
n
6
ASP
21
H
ALA
22
n
7
ALA
22
H
GLU
23
n
8
GLU
23
H
ILE
24
n
9
ILE
24
H
GLY
25
n
10
GLY
25
H
MET
26
n
11
MET
26
H
SER
27
n
12
SER
27
H
PRO
28
n
13
PRO
28
H
TRP
29
n
14
TRP
29
H
GLN
30
n
15
GLN
30
H
VAL
31
n
16
VAL
31
H
MET
32
n
17
MET
32
H
LEU
33
n
18
LEU
33
H
PHE
34
n
19
PHE
34
H
ARG
35
n
20
ARG
35
H
LYS
36
n
21
LYS
36
H
SER
36
n
22
A
SER
36
H
PRO
37
n
23
PRO
37
H
GLN
38
n
24
GLN
38
H
GLU
39
n
25
GLU
39
H
LEU
40
n
26
LEU
40
H
LEU
41
n
27
LEU
41
H
CYS
42
n
28
CYS
42
H
GLY
43
n
29
GLY
43
H
ALA
44
n
30
ALA
44
H
SER
45
n
31
SER
45
H
LEU
46
n
32
LEU
46
H
ILE
47
n
33
ILE
47
H
SER
48
n
34
SER
48
H
ASP
49
n
35
ASP
49
H
ARG
50
n
36
ARG
50
H
TRP
51
n
37
TRP
51
H
VAL
52
n
38
VAL
52
H
LEU
53
n
39
LEU
53
H
THR
54
n
40
THR
54
H
ALA
55
n
41
ALA
55
H
ALA
56
n
42
ALA
56
H
HIS
57
n
43
HIS
57
H
CYS
58
n
44
CYS
58
H
LEU
59
n
45
LEU
59
H
LEU
60
n
46
LEU
60
H
TYR
60
n
47
A
TYR
60
H
PRO
60
n
48
B
PRO
60
H
PRO
60
n
49
C
PRO
60
H
TRP
60
n
50
D
TRP
60
H
ASP
60
n
51
E
ASP
60
H
LYS
60
n
52
F
LYS
60
H
ASN
60
n
53
G
ASN
60
H
PHE
60
n
54
H
PHE
60
H
THR
60
n
55
I
THR
60
H
GLU
61
n
56
GLU
61
H
ASN
62
n
57
ASN
62
H
ASP
63
n
58
ASP
63
H
LEU
64
n
59
LEU
64
H
LEU
65
n
60
LEU
65
H
VAL
66
n
61
VAL
66
H
ARG
67
n
62
ARG
67
H
ILE
68
n
63
ILE
68
H
GLY
69
n
64
GLY
69
H
LYS
70
n
65
LYS
70
H
HIS
71
n
66
HIS
71
H
SER
72
n
67
SER
72
H
ARG
73
n
68
ARG
73
H
THR
74
n
69
THR
74
H
ARG
75
n
70
ARG
75
H
TYR
76
n
71
TYR
76
H
GLU
77
n
72
GLU
77
H
ARG
77
n
73
A
ARG
77
H
ASN
78
n
74
ASN
78
H
ILE
79
n
75
ILE
79
H
GLU
80
n
76
GLU
80
H
LYS
81
n
77
LYS
81
H
ILE
82
n
78
ILE
82
H
SER
83
n
79
SER
83
H
MET
84
n
80
MET
84
H
LEU
85
n
81
LEU
85
H
GLU
86
n
82
GLU
86
H
LYS
87
n
83
LYS
87
H
ILE
88
n
84
ILE
88
H
TYR
89
n
85
TYR
89
H
ILE
90
n
86
ILE
90
H
HIS
91
n
87
HIS
91
H
PRO
92
n
88
PRO
92
H
ARG
93
n
89
ARG
93
H
TYR
94
n
90
TYR
94
H
ASN
95
n
91
ASN
95
H
TRP
96
n
92
TRP
96
H
ARG
97
n
93
ARG
97
H
GLU
97
n
94
A
GLU
97
H
ASN
98
n
95
ASN
98
H
LEU
99
n
96
LEU
99
H
ASP
100
n
97
ASP
100
H
ARG
101
n
98
ARG
101
H
ASP
102
n
99
ASP
102
H
ILE
103
n
100
ILE
103
H
ALA
104
n
101
ALA
104
H
LEU
105
n
102
LEU
105
H
MET
106
n
103
MET
106
H
LYS
107
n
104
LYS
107
H
LEU
108
n
105
LEU
108
H
LYS
109
n
106
LYS
109
H
LYS
110
n
107
LYS
110
H
PRO
111
n
108
PRO
111
H
VAL
112
n
109
VAL
112
H
ALA
113
n
110
ALA
113
H
PHE
114
n
111
PHE
114
H
SER
115
n
112
SER
115
H
ASP
116
n
113
ASP
116
H
TYR
117
n
114
TYR
117
H
ILE
118
n
115
ILE
118
H
HIS
119
n
116
HIS
119
H
PRO
120
n
117
PRO
120
H
VAL
121
n
118
VAL
121
H
CYS
122
n
119
CYS
122
H
LEU
123
n
120
LEU
123
H
PRO
124
n
121
PRO
124
H
ASP
125
n
122
ASP
125
H
ARG
126
n
123
ARG
126
H
GLU
127
n
124
GLU
127
H
THR
128
n
125
THR
128
H
ALA
129
n
126
ALA
129
H
ALA
129
n
127
A
ALA
129
H
SER
129
n
128
B
SER
129
H
LEU
129
n
129
C
LEU
129
H
LEU
130
n
130
LEU
130
H
GLN
131
n
131
GLN
131
H
ALA
132
n
132
ALA
132
H
GLY
133
n
133
GLY
133
H
TYR
134
n
134
TYR
134
H
LYS
135
n
135
LYS
135
H
GLY
136
n
136
GLY
136
H
ARG
137
n
137
ARG
137
H
VAL
138
n
138
VAL
138
H
THR
139
n
139
THR
139
H
GLY
140
n
140
GLY
140
H
TRP
141
n
141
TRP
141
H
GLY
142
n
142
GLY
142
H
ASN
143
n
143
ASN
143
H
LEU
144
n
144
LEU
144
H
LYS
145
n
145
LYS
145
H
GLU
146
n
146
GLU
146
H
THR
147
n
147
THR
147
H
TRP
148
n
148
TRP
148
H
THR
149
n
149
THR
149
H
ALA
149
n
150
A
ALA
149
H
ASN
149
n
151
B
ASN
149
H
VAL
149
n
152
C
VAL
149
H
GLY
149
n
153
D
GLY
149
H
LYS
149
n
154
E
LYS
149
H
GLY
150
n
155
GLY
150
H
GLN
151
n
156
GLN
151
H
PRO
152
n
157
PRO
152
H
SER
153
n
158
SER
153
H
VAL
154
n
159
VAL
154
H
LEU
155
n
160
LEU
155
H
GLN
156
n
161
GLN
156
H
VAL
157
n
162
VAL
157
H
VAL
158
n
163
VAL
158
H
ASN
159
n
164
ASN
159
H
LEU
160
n
165
LEU
160
H
PRO
161
n
166
PRO
161
H
ILE
162
n
167
ILE
162
H
VAL
163
n
168
VAL
163
H
GLU
164
n
169
GLU
164
H
ARG
165
n
170
ARG
165
H
PRO
166
n
171
PRO
166
H
VAL
167
n
172
VAL
167
H
CYS
168
n
173
CYS
168
H
LYS
169
n
174
LYS
169
H
ASP
170
n
175
ASP
170
H
SER
171
n
176
SER
171
H
THR
172
n
177
THR
172
H
ARG
173
n
178
ARG
173
H
ILE
174
n
179
ILE
174
H
ARG
175
n
180
ARG
175
H
ILE
176
n
181
ILE
176
H
THR
177
n
182
THR
177
H
ASP
178
n
183
ASP
178
H
ASN
179
n
184
ASN
179
H
MET
180
n
185
MET
180
H
PHE
181
n
186
PHE
181
H
CYS
182
n
187
CYS
182
H
ALA
183
n
188
ALA
183
H
GLY
184
n
189
GLY
184
H
TYR
184
n
190
A
TYR
184
H
LYS
185
n
191
LYS
185
H
PRO
186
n
192
PRO
186
H
ASP
186
n
193
A
ASP
186
H
GLU
186
n
194
B
GLU
186
H
GLY
186
n
195
C
GLY
186
H
LYS
186
n
196
D
LYS
186
H
ARG
187
n
197
ARG
187
H
GLY
188
n
198
GLY
188
H
ASP
189
n
199
ASP
189
H
ALA
190
n
200
ALA
190
H
CYS
191
n
201
CYS
191
H
GLU
192
n
202
GLU
192
H
GLY
193
n
203
GLY
193
H
ASP
194
n
204
ASP
194
H
SER
195
n
205
SER
195
H
GLY
196
n
206
GLY
196
H
GLY
197
n
207
GLY
197
H
PRO
198
n
208
PRO
198
H
PHE
199
n
209
PHE
199
H
VAL
200
n
210
VAL
200
H
MET
201
n
211
MET
201
H
LYS
202
n
212
LYS
202
H
SER
203
n
213
SER
203
H
PRO
204
n
214
PRO
204
H
PHE
204
n
215
A
PHE
204
H
ASN
204
n
216
B
ASN
204
H
ASN
205
n
217
ASN
205
H
ARG
206
n
218
ARG
206
H
TRP
207
n
219
TRP
207
H
TYR
208
n
220
TYR
208
H
GLN
209
n
221
GLN
209
H
MET
210
n
222
MET
210
H
GLY
211
n
223
GLY
211
H
ILE
212
n
224
ILE
212
H
VAL
213
n
225
VAL
213
H
SER
214
n
226
SER
214
H
TRP
215
n
227
TRP
215
H
GLY
216
n
228
GLY
216
H
GLU
217
n
229
GLU
217
H
GLY
219
n
230
GLY
219
H
CYS
220
n
231
CYS
220
H
ASP
221
n
232
ASP
221
H
ARG
221
n
233
A
ARG
221
H
ASP
222
n
234
ASP
222
H
GLY
223
n
235
GLY
223
H
LYS
224
n
236
LYS
224
H
TYR
225
n
237
TYR
225
H
GLY
226
n
238
GLY
226
H
PHE
227
n
239
PHE
227
H
TYR
228
n
240
TYR
228
H
THR
229
n
241
THR
229
H
HIS
230
n
242
HIS
230
H
VAL
231
n
243
VAL
231
H
PHE
232
n
244
PHE
232
H
ARG
233
n
245
ARG
233
H
LEU
234
n
246
LEU
234
H
LYS
235
n
247
LYS
235
H
LYS
236
n
248
LYS
236
H
TRP
237
n
249
TRP
237
H
ILE
238
n
250
ILE
238
H
GLN
239
n
251
GLN
239
H
LYS
240
n
252
LYS
240
H
VAL
241
n
253
VAL
241
H
ILE
242
n
254
ILE
242
H
ASP
243
n
255
ASP
243
H
GLN
244
n
256
GLN
244
H
PHE
245
n
257
PHE
245
H
GLY
246
n
258
GLY
246
H
GLU
247
n
259
GLU
247
H
n
1
54
P
ASP
55
n
2
ASP
55
P
PHE
56
n
3
PHE
56
P
GLU
57
n
4
GLU
57
P
GLU
58
n
5
GLU
58
P
ILE
59
n
6
ILE
59
P
PRO
60
n
7
PRO
60
P
GLU
61
n
8
GLU
61
P
GLU
62
n
9
GLU
62
P
TYR
63
n
10
TYS
63
P
LEU
64
n
11
LEU
64
P
GLN
65
n
12
GLN
65
P
author_and_software_defined_assembly
PISA
3
trimeric
5130
-25
13680
P
TYS
63
O-SULFO-L-TYROSINE
C
TYS
10
TYR
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
H
O
TRP
29
B
O
TRP
14
H
N
LEU
46
B
N
LEU
32
H
N
SER
45
B
N
SER
31
H
O
LEU
53
B
O
LEU
39
H
O
VAL
52
B
O
VAL
38
H
N
MET
106
B
N
MET
103
H
O
LYS
107
B
O
LYS
104
H
N
GLU
86
B
N
GLU
82
H
O
LYS
81
B
O
LYS
77
H
N
ILE
68
B
N
ILE
63
H
O
ARG
67
B
O
ARG
62
H
N
MET
32
B
N
MET
17
H
O
TYR
134
B
O
TYR
134
H
N
ILE
162
B
N
ILE
167
H
O
PRO
161
B
O
PRO
166
H
N
GLY
184
B
N
GLY
189
H
O
ASN
179
B
O
ASN
184
H
N
HIS
230
B
N
HIS
242
H
O
THR
229
B
O
THR
241
H
N
ILE
212
B
N
ILE
224
H
N
ASN
205
B
N
ASN
217
H
O
SER
203
B
O
SER
213
H
O
VAL
200
B
O
VAL
210
H
N
ARG
137
B
N
ARG
137
1
P
GLY
54
C
GLY
1
1
Y
1
H
TYR
228
0.072
SIDE CHAIN
1
9.79
1.10
114.20
123.99
H
H
H
CA
CB
SG
CYS
CYS
CYS
42
42
42
N
1
8.57
1.10
114.20
122.77
H
H
H
CA
CB
SG
CYS
CYS
CYS
182
182
182
N
C
1
L
GLU
1
-128.44
-51.54
B
1
L
ALA
1
59.73
-46.78
1
L
PHE
7
-149.51
-85.34
A
1
L
LYS
14
-42.86
-17.44
D
1
L
ARG
14
-49.86
-16.23
G
1
L
LEU
14
-49.78
-12.96
J
1
L
TYR
14
-68.90
67.45
K
1
L
ILE
14
65.04
-56.14
1
H
GLU
18
39.82
48.13
1
H
ALA
22
-67.33
-152.79
1
H
SER
27
-156.67
72.93
1
H
PRO
28
-67.11
9.32
1
H
CYS
42
-170.66
-171.17
1
H
ALA
44
179.10
-170.56
A
1
H
TYR
60
-160.94
70.03
G
1
H
ASN
60
-163.36
59.78
1
H
ASN
62
-79.72
49.89
1
H
ASP
63
-154.28
2.00
1
H
LYS
70
-65.92
-177.93
1
H
HIS
71
-176.55
-30.32
1
H
ARG
75
-57.73
-174.06
1
H
GLU
77
-48.90
80.29
1
H
ILE
79
-121.12
-75.49
A
1
H
GLU
97
-137.22
-31.12
1
H
ASN
98
-158.50
18.39
1
H
ASP
116
-55.98
-4.64
1
H
LEU
130
-69.36
79.62
1
H
ASN
143
-35.10
147.50
1
H
THR
147
-42.17
106.92
1
H
PRO
152
-37.87
145.47
D
1
H
LYS
186
-54.49
-165.54
1
H
ASP
189
178.09
175.18
B
1
H
ASN
204
-150.78
6.16
1
H
SER
214
-127.94
-62.37
1
H
ASP
243
-44.58
-76.78
1
H
PHE
245
-80.43
-106.97
1
P
GLU
58
-46.82
155.06
1
P
TYS
63
-76.81
44.30
1
P
LEU
64
-158.89
59.65
0.204
0.204
2.60
8.00
9916
1
2.0
2.60
8.00
95
2597
40
0
2462
0.014
2.03
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
ALPHA-THROMBIN, HIRUGEN PEPTIDE, N-[N-[N-[4-(AMINOIMINOMETHYL)AMINO]-1-OXOBUTYL]-L -PHENYLALANYL]-L-ALLO-THREONYL-L-PHENYLALANINE, METHYL ESTER (BMS-183507), METHYL GROUP
STRUCTURE OF A RETRO-BINDING PEPTIDE INHIBITOR COMPLEXED WITH HUMAN ALPHA-THROMBIN
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
L
THR
14
A
THR
21
HELX_P
L
TYR
14
A
TYR
29
1
H1
9
B
J
H
ASP
125
B
ASP
122
HELX_P
H
LEU
130
B
LEU
130
1
H4
9
H
GLU
164
B
GLU
169
HELX_P
H
THR
172
B
THR
177
1
H5
9
H
LEU
234
B
LEU
246
HELX_P
H
ASP
243
B
ASP
255
1
H7
10
disulf
2.020
L
CYS
1
A
SG
CYS
6
1_555
H
CYS
122
B
SG
CYS
119
1_555
disulf
2.023
H
CYS
42
B
SG
CYS
28
1_555
H
CYS
58
B
SG
CYS
44
1_555
disulf
2.034
H
CYS
168
B
SG
CYS
173
1_555
H
CYS
182
B
SG
CYS
187
1_555
disulf
2.030
H
CYS
191
B
SG
CYS
201
1_555
H
CYS
220
B
SG
CYS
231
1_555
HYDROLASE/HYDROLASE INHIBITOR
SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR complex
H
SER
36
B
SER
22
A
1
H
PRO
37
B
PRO
23
-0.85
THRB_HUMAN
UNP
1
1
P00734
MAHVRGLQLPGCLALAALCSLVHSQHVFLAPQQARSLLQRVRRANTFLEEVRKGNLERECVEETCSYEEAFEALESSTAT
DVFWAKYTACETARTPRDKLAACLEGNCAEGLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHPGADLQENFCRNP
DSSTTGPWCYTTDPTVRRQECSIPVCGQDQVTVAMTPRSEGSSVNLSPPLEQCVPDRGQQYQGRLAVTTHGLPCLAWASA
QAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDFGYCDLNYCEEAVEEETGDGLDEDSDRAIEGRTATSEY
QTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRW
VLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHP
VCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKR
GDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
THRB_HUMAN
UNP
2
1
P00734
MAHVRGLQLPGCLALAALCSLVHSQHVFLAPQQARSLLQRVRRANTFLEEVRKGNLERECVEETCSYEEAFEALESSTAT
DVFWAKYTACETARTPRDKLAACLEGNCAEGLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHPGADLQENFCRNP
DSSTTGPWCYTTDPTVRRQECSIPVCGQDQVTVAMTPRSEGSSVNLSPPLEQCVPDRGQQYQGRLAVTTHGLPCLAWASA
QAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDFGYCDLNYCEEAVEEETGDGLDEDSDRAIEGRTATSEY
QTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRW
VLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHP
VCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKR
GDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
HIR3A_HIRME
UNP
3
1
P28507
GDFEEIPEEYLQ
331
363
1HDT
1
15
P00734
L
1
6
33
364
622
1HDT
16
247
P00734
H
2
1
259
54
65
1HDT
54
65
P28507
P
3
1
12
7
7
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
H
TRP
29
B
TRP
14
H
LYS
36
B
LYS
21
H
GLU
39
B
GLU
25
H
ILE
47
B
ILE
33
H
ARG
50
B
ARG
36
H
THR
54
B
THR
40
H
ILE
103
B
ILE
100
H
LYS
109
B
LYS
106
H
LYS
81
B
LYS
77
H
HIS
91
B
HIS
87
H
ASP
63
B
ASP
58
H
GLY
69
B
GLY
64
H
GLN
30
B
GLN
15
H
LYS
36
B
LYS
21
H
TYR
134
B
TYR
134
H
GLY
140
B
GLY
140
H
LEU
155
B
LEU
160
H
ILE
162
B
ILE
167
H
ASN
179
B
ASN
184
H
GLY
184
B
GLY
189
H
GLY
226
B
GLY
238
H
VAL
231
B
VAL
243
H
ASN
205
B
ASN
217
H
TRP
215
B
TRP
227
H
GLY
197
B
GLY
207
H
SER
203
B
SER
213
H
TYR
134
B
TYR
134
H
GLY
140
B
GLY
140
BINDING SITE FOR RESIDUE 0E7 H 1
Software
15
BINDING SITE FOR CHAIN P OF HIRUGEN PEPTIDE
Software
19
ACTIVE SITE
Author
4
H
HIS
57
B
HIS
43
15
1_555
H
TYR
60
B
TYR
47
A
15
1_555
H
TRP
60
B
TRP
50
D
15
1_555
H
TRP
148
B
TRP
148
15
2_565
H
ASP
189
B
ASP
199
15
1_555
H
ALA
190
B
ALA
200
15
1_555
H
CYS
191
B
CYS
201
15
1_555
H
GLU
192
B
GLU
202
15
1_555
H
SER
195
B
SER
205
15
1_555
H
VAL
213
B
VAL
225
15
1_555
H
SER
214
B
SER
226
15
1_555
H
TRP
215
B
TRP
227
15
1_555
H
GLY
216
B
GLY
228
15
1_555
H
GLU
217
B
GLU
229
15
1_555
H
GLY
219
B
GLY
230
15
1_555
H
PHE
34
B
PHE
19
19
1_555
H
LEU
65
B
LEU
60
19
1_555
H
ARG
67
B
ARG
62
19
1_555
H
ARG
73
B
ARG
68
19
1_555
H
THR
74
B
THR
69
19
1_555
H
TYR
76
B
TYR
71
19
1_555
H
LYS
81
B
LYS
77
19
1_555
H
ILE
82
B
ILE
78
19
1_555
H
MET
84
B
MET
80
19
1_555
H
PRO
92
B
PRO
88
19
3_555
H
ARG
93
B
ARG
89
19
3_555
H
GLU
97
B
GLU
94
A
19
3_555
H
ASN
98
B
ASN
95
19
3_555
H
ASP
100
B
ASP
97
19
3_555
H
ARG
175
B
ARG
180
19
3_555
P
HOH
626
G
HOH
19
1_555
P
HOH
634
G
HOH
19
1_555
P
HOH
660
G
HOH
19
1_555
P
HOH
688
G
HOH
19
1_555
H
ASP
189
B
ASP
199
4
1_555
H
SER
195
B
SER
205
4
1_555
H
GLY
216
B
GLY
228
4
1_555
H
GLY
219
B
GLY
230
4
1_555
18
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