0.011013
0.000000
0.000000
0.000000
0.011013
0.000000
0.000000
0.000000
0.007547
0.00000
0.00000
0.00000
CIS PROLINE - PRO H 37
PHE H 245 - GLY H 246 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
LEU I 10 - GLN I 11 OMEGA =359.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
RESIDUE ASN H 60G IS GLYCOSYLATED. THE SUGAR ELECTRON DENSITY IS WEAK AND NO COORDINATES ARE PRESENT FOR THE SUGAR.
Banner, D.W.
Hadvary, P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
90.800
90.800
132.500
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
C7 H8 N2
120.152
BENZAMIDINE
non-polymer
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
266
20085
20093
1939071
Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors.
1991
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
193
175
182
2226434
Geometry of binding of the benzamidine- and arginine-based inhibitors N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-pipe ridine (NAPAP) and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) to human alpha-thrombin. X-ray crystallographic determination of the NAPAP-trypsin complex and modeling of NAPAP-thrombin and MQPA-thrombin.
1990
UK
Embo J.
EMJODG
0897
0261-4189
8
3467
3475
2583108
The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.
1989
US
Protein Sci.
PRCIEI
0795
0961-8368
1
426
471
1304349
The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.
1992
US
Science
SCIEAS
0038
0036-8075
249
277
280
2374926
The structure of a complex of recombinant hirudin and human alpha-thrombin.
1990
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
206
187
195
1587268
The interaction of thrombin with fibrinogen. A structural basis for its specificity.
1992
UK
Embo J.
EMJODG
0897
0261-4189
9
2361
2365
2369893
Crystal structure of the thrombin-hirudin complex: a novel mode of serine protease inhibition.
1990
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
4096.534
ALPHA-THROMBIN (SMALL SUBUNIT)
3.4.21.5
1
man
polymer
29780.219
ALPHA-THROMBIN (LARGE SUBUNIT)
3.4.21.5
1
man
polymer
1411.465
HIRUDIN IIIA
1
syn
polymer
120.152
BENZAMIDINE
1
syn
non-polymer
18.015
water
50
nat
water
no
no
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
L
polypeptide(L)
no
no
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
H
polypeptide(L)
no
no
DFEEIPEEYLQ
DFEEIPEEYLQ
I
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
n
n
human
sample
9606
PLASMA
Homo sapiens
human
sample
9606
PLASMA
Homo sapiens
3.87
68.20
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
1
0
1994-01-31
1
1
2008-03-03
1
2
2011-07-13
Y
1992-08-19
REL
BEN
BENZAMIDINE
HOH
water
6421
medicinal leech
Hirudo medicinalis
sample
THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN
INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN
INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN
INDICATOR *I* IS USED FOR A C-TERMINAL HIRUDIN PEPTIDE
((DES-AMINO ASP55)HIRUDIN(55-65)). THE RESIDUES OF
CHAIN I ARE NUMBERED FROM 1 - 11. IT BINDS IN THE
ANION-BINDING EXOSITE.
BEN
1
4
BEN
BEN
1
H
HOH
312
5
HOH
HOH
312
L
HOH
327
5
HOH
HOH
327
L
HOH
330
5
HOH
HOH
330
L
HOH
345
5
HOH
HOH
345
L
HOH
300
5
HOH
HOH
300
H
HOH
302
5
HOH
HOH
302
H
HOH
305
5
HOH
HOH
305
H
HOH
306
5
HOH
HOH
306
H
HOH
307
5
HOH
HOH
307
H
HOH
308
5
HOH
HOH
308
H
HOH
309
5
HOH
HOH
309
H
HOH
310
5
HOH
HOH
310
H
HOH
311
5
HOH
HOH
311
H
HOH
313
5
HOH
HOH
313
H
HOH
314
5
HOH
HOH
314
H
HOH
315
5
HOH
HOH
315
H
HOH
316
5
HOH
HOH
316
H
HOH
317
5
HOH
HOH
317
H
HOH
318
5
HOH
HOH
318
H
HOH
319
5
HOH
HOH
319
H
HOH
320
5
HOH
HOH
320
H
HOH
321
5
HOH
HOH
321
H
HOH
322
5
HOH
HOH
322
H
HOH
323
5
HOH
HOH
323
H
HOH
324
5
HOH
HOH
324
H
HOH
325
5
HOH
HOH
325
H
HOH
326
5
HOH
HOH
326
H
HOH
328
5
HOH
HOH
328
H
HOH
329
5
HOH
HOH
329
H
HOH
331
5
HOH
HOH
331
H
HOH
332
5
HOH
HOH
332
H
HOH
333
5
HOH
HOH
333
H
HOH
334
5
HOH
HOH
334
H
HOH
335
5
HOH
HOH
335
H
HOH
336
5
HOH
HOH
336
H
HOH
337
5
HOH
HOH
337
H
HOH
338
5
HOH
HOH
338
H
HOH
339
5
HOH
HOH
339
H
HOH
340
5
HOH
HOH
340
H
HOH
341
5
HOH
HOH
341
H
HOH
342
5
HOH
HOH
342
H
HOH
343
5
HOH
HOH
343
H
HOH
344
5
HOH
HOH
344
H
HOH
346
5
HOH
HOH
346
H
HOH
347
5
HOH
HOH
347
H
HOH
298
5
HOH
HOH
298
I
HOH
299
5
HOH
HOH
299
I
HOH
301
5
HOH
HOH
301
I
HOH
303
5
HOH
HOH
303
I
HOH
304
5
HOH
HOH
304
I
n
1
H
1
L
n
2
G
1
L
n
3
F
1
L
n
4
E
1
L
n
5
D
1
L
GLU
1
n
6
C
GLU
1
L
ALA
1
n
7
B
ALA
1
L
ASP
1
n
8
A
ASP
1
L
CYS
1
n
9
CYS
1
L
GLY
2
n
10
GLY
2
L
LEU
3
n
11
LEU
3
L
ARG
4
n
12
ARG
4
L
PRO
5
n
13
PRO
5
L
LEU
6
n
14
LEU
6
L
PHE
7
n
15
PHE
7
L
GLU
8
n
16
GLU
8
L
LYS
9
n
17
LYS
9
L
LYS
10
n
18
LYS
10
L
SER
11
n
19
SER
11
L
LEU
12
n
20
LEU
12
L
GLU
13
n
21
GLU
13
L
ASP
14
n
22
ASP
14
L
LYS
14
n
23
A
LYS
14
L
THR
14
n
24
B
THR
14
L
GLU
14
n
25
C
GLU
14
L
ARG
14
n
26
D
ARG
14
L
GLU
14
n
27
E
GLU
14
L
LEU
14
n
28
F
LEU
14
L
LEU
14
n
29
G
LEU
14
L
GLU
14
n
30
H
GLU
14
L
SER
14
n
31
I
SER
14
L
TYR
14
n
32
J
TYR
14
L
ILE
14
n
33
K
ILE
14
L
ASP
14
n
34
L
ASP
14
L
n
35
M
14
L
n
36
N
14
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
n
259
247
H
ASP
1
n
1
ASP
1
I
PHE
2
n
2
PHE
2
I
GLU
3
n
3
GLU
3
I
GLU
4
n
4
GLU
4
I
ILE
5
n
5
ILE
5
I
PRO
6
n
6
PRO
6
I
GLU
7
n
7
GLU
7
I
GLU
8
n
8
GLU
8
I
TYR
9
n
9
TYR
9
I
LEU
10
n
10
LEU
10
I
GLN
11
n
11
GLN
11
I
author_and_software_defined_assembly
PISA
3
trimeric
3640
-13
13570
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
N
ARG
35
B
N
ARG
20
H
O
GLU
39
B
O
GLU
25
H
N
ILE
47
B
N
ILE
33
H
O
TRP
51
B
O
TRP
37
H
N
THR
54
B
N
THR
40
H
O
ALA
104
B
O
ALA
101
H
O
LYS
107
B
O
LYS
104
H
N
GLU
86
B
N
GLU
82
H
N
LEU
85
B
N
LEU
81
H
O
LEU
64
B
O
LEU
59
H
O
ARG
67
B
O
ARG
62
H
N
MET
32
B
N
MET
17
C
1
L
CG
GLU
1
A
CG
GLU
6
1
Y
C
1
L
CD
GLU
1
A
CD
GLU
6
1
Y
C
1
L
OE1
GLU
1
A
OE1
GLU
6
1
Y
C
1
L
OE2
GLU
1
A
OE2
GLU
6
1
Y
A
1
H
CG
ARG
77
B
CG
ARG
73
1
Y
A
1
H
CD
ARG
77
B
CD
ARG
73
1
Y
A
1
H
NE
ARG
77
B
NE
ARG
73
1
Y
A
1
H
CZ
ARG
77
B
CZ
ARG
73
1
Y
A
1
H
NH1
ARG
77
B
NH1
ARG
73
1
Y
A
1
H
NH2
ARG
77
B
NH2
ARG
73
1
Y
1
H
CG
ASN
78
B
CG
ASN
74
1
Y
1
H
OD1
ASN
78
B
OD1
ASN
74
1
Y
1
H
ND2
ASN
78
B
ND2
ASN
74
1
Y
1
H
CG
LYS
81
B
CG
LYS
77
1
Y
1
H
CD
LYS
81
B
CD
LYS
77
1
Y
1
H
CE
LYS
81
B
CE
LYS
77
1
Y
1
H
NZ
LYS
81
B
NZ
LYS
77
1
Y
1
H
CG
ARG
93
B
CG
ARG
89
1
Y
1
H
CD
ARG
93
B
CD
ARG
89
1
Y
1
H
NE
ARG
93
B
NE
ARG
89
1
Y
1
H
CZ
ARG
93
B
CZ
ARG
89
1
Y
1
H
NH1
ARG
93
B
NH1
ARG
89
1
Y
1
H
NH2
ARG
93
B
NH2
ARG
89
1
Y
1
H
CG
ARG
97
B
CG
ARG
93
1
Y
1
H
CD
ARG
97
B
CD
ARG
93
1
Y
1
H
NE
ARG
97
B
NE
ARG
93
1
Y
1
H
CZ
ARG
97
B
CZ
ARG
93
1
Y
1
H
NH1
ARG
97
B
NH1
ARG
93
1
Y
1
H
NH2
ARG
97
B
NH2
ARG
93
1
Y
1
H
CG
GLU
127
B
CG
GLU
124
1
Y
1
H
CD
GLU
127
B
CD
GLU
124
1
Y
1
H
OE1
GLU
127
B
OE1
GLU
124
1
Y
1
H
OE2
GLU
127
B
OE2
GLU
124
1
Y
E
1
H
CG
LYS
149
B
CG
LYS
154
1
Y
E
1
H
CD
LYS
149
B
CD
LYS
154
1
Y
E
1
H
CE
LYS
149
B
CE
LYS
154
1
Y
E
1
H
NZ
LYS
149
B
NZ
LYS
154
1
Y
1
H
CG
LYS
169
B
CG
LYS
174
1
Y
1
H
CD
LYS
169
B
CD
LYS
174
1
Y
1
H
CE
LYS
169
B
CE
LYS
174
1
Y
1
H
NZ
LYS
169
B
NZ
LYS
174
1
Y
1
H
CG
ARG
173
B
CG
ARG
178
1
Y
1
H
CD
ARG
173
B
CD
ARG
178
1
Y
1
H
NE
ARG
173
B
NE
ARG
178
1
Y
1
H
CZ
ARG
173
B
CZ
ARG
178
1
Y
1
H
NH1
ARG
173
B
NH1
ARG
178
1
Y
1
H
NH2
ARG
173
B
NH2
ARG
178
1
Y
1
H
CA
GLY
246
B
CA
GLY
258
1
Y
1
H
C
GLY
246
B
C
GLY
258
1
Y
1
H
O
GLY
246
B
O
GLY
258
1
Y
1
I
N
ASP
1
C
N
ASP
1
1
Y
1
I
CG
GLU
8
C
CG
GLU
8
1
Y
1
I
CD
GLU
8
C
CD
GLU
8
1
Y
1
I
OE1
GLU
8
C
OE1
GLU
8
1
Y
1
I
OE2
GLU
8
C
OE2
GLU
8
1
Y
1
I
CA
GLN
11
C
CA
GLN
11
1
Y
1
I
C
GLN
11
C
C
GLN
11
1
Y
1
I
O
GLN
11
C
O
GLN
11
1
Y
1
I
CB
GLN
11
C
CB
GLN
11
1
Y
1
I
CG
GLN
11
C
CG
GLN
11
1
Y
1
I
CD
GLN
11
C
CD
GLN
11
1
Y
1
I
OE1
GLN
11
C
OE1
GLN
11
1
Y
1
I
NE2
GLN
11
C
NE2
GLN
11
1
Y
H
1
L
THR
1
A
THR
1
1
Y
G
1
L
PHE
1
A
PHE
2
1
Y
F
1
L
GLY
1
A
GLY
3
1
Y
E
1
L
SER
1
A
SER
4
1
Y
D
1
L
GLY
1
A
GLY
5
1
Y
M
1
L
GLY
14
A
GLY
35
1
Y
N
1
L
ARG
14
A
ARG
36
1
Y
1
H
GLU
247
B
GLU
259
1
Y
L
L
L
1
5.66
0.90
118.30
123.96
L
L
L
CB
CG
OD1
ASP
ASP
ASP
14
14
14
N
L
L
L
1
-6.68
0.90
118.30
111.62
L
L
L
CB
CG
OD2
ASP
ASP
ASP
14
14
14
N
1
-11.18
1.80
110.60
99.42
H
H
H
N
CA
CB
ASP
ASP
ASP
49
49
49
N
1
-6.69
0.90
118.30
111.61
H
H
H
CB
CG
OD2
ASP
ASP
ASP
49
49
49
N
E
E
E
1
5.54
0.90
118.30
123.84
H
H
H
CB
CG
OD1
ASP
ASP
ASP
60
60
60
N
E
E
E
1
-7.08
0.90
118.30
111.22
H
H
H
CB
CG
OD2
ASP
ASP
ASP
60
60
60
N
1
-3.34
0.50
120.30
116.96
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
101
101
101
N
1
-5.74
0.90
118.30
112.56
H
H
H
CB
CG
OD2
ASP
ASP
ASP
102
102
102
N
1
-5.68
0.90
118.30
112.62
H
H
H
CB
CG
OD2
ASP
ASP
ASP
170
170
170
N
1
5.48
0.90
118.30
123.78
H
H
H
CB
CG
OD1
ASP
ASP
ASP
178
178
178
N
1
-6.05
0.90
118.30
112.25
H
H
H
CB
CG
OD2
ASP
ASP
ASP
178
178
178
N
1
-6.51
0.90
118.30
111.79
H
H
H
CB
CG
OD1
ASP
ASP
ASP
189
189
189
N
1
6.42
0.90
118.30
124.72
H
H
H
CB
CG
OD2
ASP
ASP
ASP
189
189
189
N
1
-5.82
0.90
118.30
112.48
H
H
H
CB
CG
OD1
ASP
ASP
ASP
194
194
194
N
1
-5.40
0.90
118.30
112.90
H
H
H
CB
CG
OD2
ASP
ASP
ASP
243
243
243
N
E
E
1
L
L
CD
OE1
GLU
GLU
14
14
0.071
0.011
1.252
1.323
N
1
H
H
CD
OE2
GLU
GLU
18
18
0.073
0.011
1.252
1.325
N
1
H
H
CD
OE2
GLU
GLU
39
39
0.070
0.011
1.252
1.322
N
1
H
H
CD
OE2
GLU
GLU
86
86
0.069
0.011
1.252
1.321
N
A
A
1
H
H
CD
OE1
GLU
GLU
97
97
0.070
0.011
1.252
1.322
N
B
B
1
H
H
CD
OE2
GLU
GLU
186
186
0.076
0.011
1.252
1.328
N
1
I
I
CD
OE2
GLU
GLU
4
4
0.075
0.011
1.252
1.327
N
1
L
PHE
7
-126.42
-87.59
1
H
SER
48
175.36
166.10
1
H
ASP
49
-36.70
-22.82
1
H
ARG
50
-146.85
-0.47
1
H
HIS
57
-51.74
-5.36
A
1
H
TYR
60
-155.91
82.23
C
1
H
PRO
60
-35.29
-22.00
G
1
H
ASN
60
-154.95
72.57
1
H
HIS
71
-123.55
-57.42
B
1
H
ASN
149
62.57
-6.77
C
1
H
VAL
149
-105.63
71.63
1
H
SER
214
-104.45
-73.31
1
H
GLN
244
-58.34
6.57
PROLINES ARE TOO FLAT AS A BAD DICTIONARY WAS USED.
ASN H 60G IS GLYCOSYLATED. THE SUGAR ELECTRON DENSITY IS
WEAK AND NO COORDINATES ARE PRESENT FOR THE SUGAR.
0.151
3.16
25.0
1
0.0
3.16
25.0
50
2417
9
0
2358
0.015
1.93
refinement
TNT
ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX WITH (DES-AMINO ASP 55) HIRUDIN (RESIDUES 55 - 65) AND BENZAMIDINE
CRYSTALLOGRAPHIC ANALYSIS AT 3.0-ANGSTROMS RESOLUTION OF THE BINDING TO HUMAN THROMBIN OF FOUR ACTIVE SITE-DIRECTED INHIBITORS
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
L
PHE
7
A
PHE
15
HELX_P
L
SER
11
A
SER
19
5
1
5
L
THR
14
A
THR
24
HELX_P
L
SER
14
A
SER
31
1
2
8
B
I
H
ALA
55
B
ALA
41
HELX_P
H
CYS
58
B
CYS
44
5
3
4
H
PRO
60
B
PRO
48
HELX_P
H
ASP
60
B
ASP
51
5
4
4
B
E
H
ASP
125
B
ASP
122
HELX_P
H
LEU
130
B
LEU
130
1
5
9
H
GLU
164
B
GLU
169
HELX_P
H
ASP
170
B
ASP
175
1
6
7
H
LYS
185
B
LYS
191
HELX_P
H
GLY
186
B
GLY
195
5
7
5
C
H
LEU
234
B
LEU
246
HELX_P
H
ASP
243
B
ASP
255
1
8
10
I
PRO
6
C
PRO
6
HELX_P
I
LEU
10
C
LEU
10
5
9
5
disulf
2.012
L
CYS
1
A
SG
CYS
9
1_555
H
CYS
122
B
SG
CYS
119
1_555
disulf
2.064
H
CYS
42
B
SG
CYS
28
1_555
H
CYS
58
B
SG
CYS
44
1_555
disulf
2.029
H
CYS
168
B
SG
CYS
173
1_555
H
CYS
182
B
SG
CYS
187
1_555
disulf
2.043
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
0.80
THRB_HUMAN
UNP
1
328
P00734
THRB_HUMAN
UNP
2
364
P00734
ITHH_HIRME
UNP
3
55
P28508
328
363
1DWB
1
14
P00734
H
N
L
1
1
36
364
622
1DWB
16
247
P00734
H
2
1
259
55
65
1DWB
1
11
P28508
I
3
1
11
7
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
H
GLN
30
B
GLN
15
H
ARG
35
B
ARG
20
H
GLU
39
B
GLU
25
H
SER
48
B
SER
34
H
TRP
51
B
TRP
37
H
THR
54
B
THR
40
H
ALA
104
B
ALA
101
H
LEU
108
B
LEU
105
H
LYS
81
B
LYS
77
H
ILE
90
B
ILE
86
H
LEU
64
B
LEU
59
H
ILE
68
B
ILE
63
H
GLN
30
B
GLN
15
H
ARG
35
B
ARG
20
CATALYTIC SITE
Author
3
BINDING SITE FOR RESIDUE BEN H 1
Software
7
BINDING SITE FOR CHAIN I OF HIRUDIN IIIA
Software
18
H
HIS
57
B
HIS
43
3
1_555
H
ASP
102
B
ASP
99
3
1_555
H
SER
195
B
SER
205
3
1_555
H
ASP
189
B
ASP
199
7
1_555
H
ALA
190
B
ALA
200
7
1_555
H
SER
195
B
SER
205
7
1_555
H
TRP
215
B
TRP
227
7
1_555
H
GLY
219
B
GLY
230
7
1_555
H
GLY
226
B
GLY
238
7
1_555
H
HOH
325
F
HOH
7
1_555
H
LYS
36
B
LYS
21
18
1_555
H
GLN
38
B
GLN
24
18
1_555
H
ARG
67
B
ARG
62
18
1_555
H
ARG
73
B
ARG
68
18
1_555
H
THR
74
B
THR
69
18
1_555
H
ARG
75
B
ARG
70
18
7_555
H
ARG
75
B
ARG
70
18
1_555
H
TYR
76
B
TYR
71
18
1_555
H
ILE
82
B
ILE
78
18
1_555
H
MET
84
B
MET
80
18
1_555
H
LYS
236
B
LYS
248
18
3_544
H
GLN
239
B
GLN
251
18
3_544
H
HOH
339
F
HOH
18
1_555
I
HOH
298
G
HOH
18
1_555
I
HOH
299
G
HOH
18
1_555
I
HOH
301
G
HOH
18
7_555
I
HOH
303
G
HOH
18
1_555
I
HOH
304
G
HOH
18
1_555
96
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