0.013937
0.000000
0.002775
0.000000
0.013814
0.000000
0.000000
0.000000
0.013869
0.00000
0.00000
0.00000
CIS PROLINE - PRO H 37
RESIDUE TYR I 63 IN THE HIRUGEN MOLECULE IS BONDED TO SULFATO- TYROSINE.
Tulinsky, A.
Vijayalakshmi, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
101.26
90.00
71.750
72.390
73.520
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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
D-saccharide, beta 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
US
Protein Sci.
PRCIEI
0795
0961-8368
3
2254
2271
7756983
The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin.
1994
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
221
583
Refined Structure of the Hirudin-Thrombin Complex
1991
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
221
1379
Structure of the Hirugen and Hirulog 1 Complexes of Alpha-Thrombin
1991
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
1363.399
HIRUGEN
1
man
polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
18.015
water
204
nat
water
no
no
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
L
polypeptide(L)
no
no
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM
LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE
H
polypeptide(L)
no
yes
DFEEIPEE(TYS)L
DFEEIPEEYL
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
human
Homo
sample
9606
Homo sapiens
human
Homo
sample
9606
Homo sapiens
medicinal leech
Hirudo
sample
6421
Hirudo medicinalis
2.66
53.79
pdbx_database_status
struct_conf
struct_conf_type
software
struct_conn
software
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_conn
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Non-polymer description
Version format compliance
Derived calculations
Other
Data collection
Derived calculations
Refinement description
Data collection
Refinement description
Data collection
Derived calculations
Structure summary
1
0
1994-12-20
1
1
2008-03-03
1
2
2011-07-13
1
3
2017-11-29
1
4
2019-07-17
1
5
2019-08-14
1
6
2020-07-29
_pdbx_database_status.process_site
_software.classification
_struct_conn.pdbx_leaving_atom_flag
_software.classification
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_role
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
SHEET
THE SHEET PRESENTED AS *B1* ON SHEET RECORDS BELOW IS
ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED
BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST
STRANDS ARE IDENTICAL. THE SHEET PRESENTED AS *B2* ON
SHEET RECORDS BELOW IS ACTUALLY A SEVEN-STRANDED
BETA-BARREL. THIS IS REPRESENTED BY AN EIGHT-STRANDED
SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.
Y
BNL
1994-06-27
REL
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
HOH
water
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 N-ACETYLHIRUDIN 53 - 64 WITH
SULFATO-TYR 63.
PEPTIDE ASP I 55 - LEU I 64 AT THE EXOSITE OF THROMBIN IS
HIRUGEN MOLECULE, WHICH IS PART OF HIRUDIN 53 - 65.
NAG
400
4
NAG
NAG
400
H
HOH
432
5
HOH
HOH
432
L
HOH
439
5
HOH
HOH
439
L
HOH
440
5
HOH
HOH
440
L
HOH
449
5
HOH
HOH
449
L
HOH
452
5
HOH
HOH
452
L
HOH
465
5
HOH
HOH
465
L
HOH
468
5
HOH
HOH
468
L
HOH
470
5
HOH
HOH
470
L
HOH
474
5
HOH
HOH
474
L
HOH
485
5
HOH
HOH
485
L
HOH
511
5
HOH
HOH
511
L
HOH
514
5
HOH
HOH
514
L
HOH
534
5
HOH
HOH
534
L
HOH
540
5
HOH
HOH
540
L
HOH
543
5
HOH
HOH
543
L
HOH
552
5
HOH
HOH
552
L
HOH
557
5
HOH
HOH
557
L
HOH
560
5
HOH
HOH
560
L
HOH
567
5
HOH
HOH
567
L
HOH
575
5
HOH
HOH
575
L
HOH
590
5
HOH
HOH
590
L
HOH
599
5
HOH
HOH
599
L
HOH
600
5
HOH
HOH
600
L
HOH
602
5
HOH
HOH
602
L
HOH
401
5
HOH
HOH
401
H
HOH
402
5
HOH
HOH
402
H
HOH
403
5
HOH
HOH
403
H
HOH
404
5
HOH
HOH
404
H
HOH
405
5
HOH
HOH
405
H
HOH
406
5
HOH
HOH
406
H
HOH
407
5
HOH
HOH
407
H
HOH
408
5
HOH
HOH
408
H
HOH
409
5
HOH
HOH
409
H
HOH
410
5
HOH
HOH
410
H
HOH
411
5
HOH
HOH
411
H
HOH
412
5
HOH
HOH
412
H
HOH
413
5
HOH
HOH
413
H
HOH
414
5
HOH
HOH
414
H
HOH
415
5
HOH
HOH
415
H
HOH
416
5
HOH
HOH
416
H
HOH
417
5
HOH
HOH
417
H
HOH
418
5
HOH
HOH
418
H
HOH
419
5
HOH
HOH
419
H
HOH
420
5
HOH
HOH
420
H
HOH
421
5
HOH
HOH
421
H
HOH
422
5
HOH
HOH
422
H
HOH
423
5
HOH
HOH
423
H
HOH
424
5
HOH
HOH
424
H
HOH
425
5
HOH
HOH
425
H
HOH
426
5
HOH
HOH
426
H
HOH
427
5
HOH
HOH
427
H
HOH
428
5
HOH
HOH
428
H
HOH
429
5
HOH
HOH
429
H
HOH
430
5
HOH
HOH
430
H
HOH
431
5
HOH
HOH
431
H
HOH
433
5
HOH
HOH
433
H
HOH
434
5
HOH
HOH
434
H
HOH
435
5
HOH
HOH
435
H
HOH
436
5
HOH
HOH
436
H
HOH
437
5
HOH
HOH
437
H
HOH
438
5
HOH
HOH
438
H
HOH
441
5
HOH
HOH
441
H
HOH
442
5
HOH
HOH
442
H
HOH
443
5
HOH
HOH
443
H
HOH
444
5
HOH
HOH
444
H
HOH
445
5
HOH
HOH
445
H
HOH
446
5
HOH
HOH
446
H
HOH
447
5
HOH
HOH
447
H
HOH
448
5
HOH
HOH
448
H
HOH
450
5
HOH
HOH
450
H
HOH
451
5
HOH
HOH
451
H
HOH
454
5
HOH
HOH
454
H
HOH
455
5
HOH
HOH
455
H
HOH
456
5
HOH
HOH
456
H
HOH
457
5
HOH
HOH
457
H
HOH
458
5
HOH
HOH
458
H
HOH
459
5
HOH
HOH
459
H
HOH
460
5
HOH
HOH
460
H
HOH
461
5
HOH
HOH
461
H
HOH
462
5
HOH
HOH
462
H
HOH
463
5
HOH
HOH
463
H
HOH
464
5
HOH
HOH
464
H
HOH
466
5
HOH
HOH
466
H
HOH
467
5
HOH
HOH
467
H
HOH
469
5
HOH
HOH
469
H
HOH
471
5
HOH
HOH
471
H
HOH
472
5
HOH
HOH
472
H
HOH
473
5
HOH
HOH
473
H
HOH
475
5
HOH
HOH
475
H
HOH
476
5
HOH
HOH
476
H
HOH
477
5
HOH
HOH
477
H
HOH
478
5
HOH
HOH
478
H
HOH
479
5
HOH
HOH
479
H
HOH
480
5
HOH
HOH
480
H
HOH
481
5
HOH
HOH
481
H
HOH
482
5
HOH
HOH
482
H
HOH
483
5
HOH
HOH
483
H
HOH
484
5
HOH
HOH
484
H
HOH
486
5
HOH
HOH
486
H
HOH
487
5
HOH
HOH
487
H
HOH
488
5
HOH
HOH
488
H
HOH
489
5
HOH
HOH
489
H
HOH
490
5
HOH
HOH
490
H
HOH
491
5
HOH
HOH
491
H
HOH
492
5
HOH
HOH
492
H
HOH
493
5
HOH
HOH
493
H
HOH
494
5
HOH
HOH
494
H
HOH
495
5
HOH
HOH
495
H
HOH
496
5
HOH
HOH
496
H
HOH
497
5
HOH
HOH
497
H
HOH
498
5
HOH
HOH
498
H
HOH
500
5
HOH
HOH
500
H
HOH
501
5
HOH
HOH
501
H
HOH
502
5
HOH
HOH
502
H
HOH
503
5
HOH
HOH
503
H
HOH
504
5
HOH
HOH
504
H
HOH
505
5
HOH
HOH
505
H
HOH
506
5
HOH
HOH
506
H
HOH
507
5
HOH
HOH
507
H
HOH
508
5
HOH
HOH
508
H
HOH
509
5
HOH
HOH
509
H
HOH
510
5
HOH
HOH
510
H
HOH
512
5
HOH
HOH
512
H
HOH
513
5
HOH
HOH
513
H
HOH
515
5
HOH
HOH
515
H
HOH
516
5
HOH
HOH
516
H
HOH
517
5
HOH
HOH
517
H
HOH
518
5
HOH
HOH
518
H
HOH
519
5
HOH
HOH
519
H
HOH
520
5
HOH
HOH
520
H
HOH
521
5
HOH
HOH
521
H
HOH
522
5
HOH
HOH
522
H
HOH
523
5
HOH
HOH
523
H
HOH
524
5
HOH
HOH
524
H
HOH
525
5
HOH
HOH
525
H
HOH
526
5
HOH
HOH
526
H
HOH
527
5
HOH
HOH
527
H
HOH
528
5
HOH
HOH
528
H
HOH
529
5
HOH
HOH
529
H
HOH
530
5
HOH
HOH
530
H
HOH
531
5
HOH
HOH
531
H
HOH
532
5
HOH
HOH
532
H
HOH
533
5
HOH
HOH
533
H
HOH
536
5
HOH
HOH
536
H
HOH
537
5
HOH
HOH
537
H
HOH
538
5
HOH
HOH
538
H
HOH
539
5
HOH
HOH
539
H
HOH
541
5
HOH
HOH
541
H
HOH
542
5
HOH
HOH
542
H
HOH
544
5
HOH
HOH
544
H
HOH
545
5
HOH
HOH
545
H
HOH
546
5
HOH
HOH
546
H
HOH
547
5
HOH
HOH
547
H
HOH
548
5
HOH
HOH
548
H
HOH
549
5
HOH
HOH
549
H
HOH
550
5
HOH
HOH
550
H
HOH
551
5
HOH
HOH
551
H
HOH
553
5
HOH
HOH
553
H
HOH
554
5
HOH
HOH
554
H
HOH
555
5
HOH
HOH
555
H
HOH
556
5
HOH
HOH
556
H
HOH
558
5
HOH
HOH
558
H
HOH
559
5
HOH
HOH
559
H
HOH
561
5
HOH
HOH
561
H
HOH
562
5
HOH
HOH
562
H
HOH
563
5
HOH
HOH
563
H
HOH
564
5
HOH
HOH
564
H
HOH
565
5
HOH
HOH
565
H
HOH
566
5
HOH
HOH
566
H
HOH
568
5
HOH
HOH
568
H
HOH
569
5
HOH
HOH
569
H
HOH
570
5
HOH
HOH
570
H
HOH
571
5
HOH
HOH
571
H
HOH
572
5
HOH
HOH
572
H
HOH
573
5
HOH
HOH
573
H
HOH
574
5
HOH
HOH
574
H
HOH
576
5
HOH
HOH
576
H
HOH
577
5
HOH
HOH
577
H
HOH
578
5
HOH
HOH
578
H
HOH
579
5
HOH
HOH
579
H
HOH
580
5
HOH
HOH
580
H
HOH
581
5
HOH
HOH
581
H
HOH
582
5
HOH
HOH
582
H
HOH
583
5
HOH
HOH
583
H
HOH
584
5
HOH
HOH
584
H
HOH
585
5
HOH
HOH
585
H
HOH
586
5
HOH
HOH
586
H
HOH
587
5
HOH
HOH
587
H
HOH
588
5
HOH
HOH
588
H
HOH
589
5
HOH
HOH
589
H
HOH
591
5
HOH
HOH
591
H
HOH
592
5
HOH
HOH
592
H
HOH
593
5
HOH
HOH
593
H
HOH
594
5
HOH
HOH
594
H
HOH
595
5
HOH
HOH
595
H
HOH
596
5
HOH
HOH
596
H
HOH
597
5
HOH
HOH
597
H
HOH
598
5
HOH
HOH
598
H
HOH
601
5
HOH
HOH
601
H
HOH
603
5
HOH
HOH
603
H
HOH
604
5
HOH
HOH
604
H
HOH
605
5
HOH
HOH
605
H
HOH
499
5
HOH
HOH
499
I
HOH
535
5
HOH
HOH
535
I
THR
1
n
1
H
THR
1
L
PHE
1
n
2
G
PHE
1
L
GLY
1
n
3
F
GLY
1
L
SER
1
n
4
E
SER
1
L
GLY
1
n
5
D
GLY
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
GLY
14
n
35
M
GLY
14
L
ARG
15
n
36
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
n
149
A
148
H
n
150
B
148
H
n
151
C
148
H
n
152
D
148
H
n
153
E
148
H
n
154
F
148
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
ASP
55
n
1
ASP
55
I
PHE
56
n
2
PHE
56
I
GLU
57
n
3
GLU
57
I
GLU
58
n
4
GLU
58
I
ILE
59
n
5
ILE
59
I
PRO
60
n
6
PRO
60
I
GLU
61
n
7
GLU
61
I
GLU
62
n
8
GLU
62
I
TYS
63
n
9
TYS
63
I
LEU
64
n
10
LEU
64
I
author_and_software_defined_assembly
PISA
3
trimeric
4450
-17
13220
G
H
ASN
60
GLYCOSYLATION SITE
B
ASN
53
ASN
I
TYS
63
O-SULFO-L-TYROSINE
C
TYS
9
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
1
H
HOH
508
F
HOH
1
H
HOH
518
F
HOH
A
1
H
THR
148
B
THR
149
1
Y
B
1
H
ALA
148
B
ALA
150
1
Y
C
1
H
ASN
148
B
ASN
151
1
Y
D
1
H
VAL
148
B
VAL
152
1
Y
E
1
H
GLY
148
B
GLY
153
1
Y
F
1
H
LYS
148
B
LYS
154
1
Y
1
L
PRO
5
-10.35
1
H
ILE
16
-11.74
1
H
LEU
160
-10.51
1
H
GLY
188
-11.67
D
1
L
ARG
14
0.227
SIDE CHAIN
1
L
ARG
15
0.133
SIDE CHAIN
1
H
ARG
50
0.202
SIDE CHAIN
1
H
ARG
101
0.101
SIDE CHAIN
1
H
ASP
102
0.080
SIDE CHAIN
1
H
ARG
173
0.137
SIDE CHAIN
1
H
ARG
187
0.121
SIDE CHAIN
F
F
F
1
-12.05
1.80
120.60
108.55
L
L
L
CA
C
O
GLY
GLY
GLY
1
1
1
N
A
A
A
1
-8.76
0.90
118.30
109.54
L
L
L
CB
CG
OD1
ASP
ASP
ASP
1
1
1
N
A
A
A
1
7.44
0.90
118.30
125.74
L
L
L
CB
CG
OD2
ASP
ASP
ASP
1
1
1
N
1
-6.66
1.10
119.40
112.74
L
L
L
NH1
CZ
NH2
ARG
ARG
ARG
4
4
4
N
1
3.87
0.50
120.30
124.17
L
L
L
NE
CZ
NH2
ARG
ARG
ARG
4
4
4
N
D
D
D
1
10.57
1.40
123.60
134.17
L
L
L
CD
NE
CZ
ARG
ARG
ARG
14
14
14
N
D
D
D
1
5.32
0.50
120.30
125.62
L
L
L
NE
CZ
NH2
ARG
ARG
ARG
14
14
14
N
H
H
H
1
9.10
1.20
123.30
132.40
L
L
L
OE1
CD
OE2
GLU
GLU
GLU
14
14
14
N
K
L
L
1
15.09
2.50
121.70
136.79
L
L
L
C
N
CA
ILE
ASP
ASP
14
14
14
Y
M
1
24.47
2.50
121.70
146.17
L
L
L
C
N
CA
GLY
ARG
ARG
14
15
15
Y
1
19.89
1.40
123.60
143.49
L
L
L
CD
NE
CZ
ARG
ARG
ARG
15
15
15
N
1
14.93
0.50
120.30
135.23
L
L
L
NE
CZ
NH1
ARG
ARG
ARG
15
15
15
N
1
-10.45
0.50
120.30
109.85
L
L
L
NE
CZ
NH2
ARG
ARG
ARG
15
15
15
N
1
-12.49
2.00
118.30
105.81
H
H
H
CG
CD
OE2
GLU
GLU
GLU
18
18
18
N
1
10.38
1.50
110.50
120.88
H
H
H
N
CA
CB
SER
SER
SER
20
20
20
N
1
5.79
0.90
118.30
124.09
H
H
H
CB
CG
OD1
ASP
ASP
ASP
21
21
21
N
1
-10.20
0.90
118.30
108.10
H
H
H
CB
CG
OD2
ASP
ASP
ASP
21
21
21
N
1
12.97
1.50
110.50
123.47
H
H
H
N
CA
CB
SER
SER
SER
27
27
27
N
1
11.56
1.90
110.20
121.76
H
H
H
CB
CA
C
LEU
LEU
LEU
33
33
33
N
1
-14.29
1.70
111.00
96.71
H
H
H
CB
CG
CD2
LEU
LEU
LEU
33
33
33
N
1
-6.99
0.50
120.30
113.31
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
35
35
35
N
1
-7.00
0.90
118.30
111.30
H
H
H
CB
CG
OD2
ASP
ASP
ASP
49
49
49
N
1
-7.77
0.50
120.30
112.53
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
50
50
50
B
B
B
N
A
A
A
1
3.75
0.60
121.00
124.75
H
H
H
CB
CG
CD2
TYR
TYR
TYR
60
60
60
N
A
A
A
1
-5.91
0.60
121.00
115.09
H
H
H
CB
CG
CD1
TYR
TYR
TYR
60
60
60
N
E
E
E
1
-5.47
0.90
118.30
112.83
H
H
H
CB
CG
OD1
ASP
ASP
ASP
60
60
60
N
H
H
H
1
-4.51
0.70
120.80
116.29
H
H
H
CB
CG
CD1
PHE
PHE
PHE
60
60
60
N
I
I
I
1
9.89
1.40
112.40
122.29
H
H
H
CA
CB
CG2
THR
THR
THR
60
60
60
N
1
10.47
1.20
123.30
133.77
H
H
H
OE1
CD
OE2
GLU
GLU
GLU
61
61
61
N
1
15.78
2.50
121.70
137.48
H
H
H
C
N
CA
VAL
ARG
ARG
66
67
67
Y
1
3.34
0.50
120.30
123.64
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
73
73
73
N
1
19.30
2.10
111.80
131.10
H
H
H
CG
CD
NE
ARG
ARG
ARG
75
75
75
B
B
B
N
1
25.30
1.40
123.60
148.90
H
H
H
CD
NE
CZ
ARG
ARG
ARG
75
75
75
B
B
B
N
1
-3.29
0.50
120.30
117.01
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
75
75
75
A
A
A
N
1
3.31
0.50
120.30
123.61
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
75
75
75
A
A
A
N
1
3.65
0.50
120.30
123.95
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
75
75
75
B
B
B
N
A
A
A
1
3.08
0.50
120.30
123.38
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
77
77
77
N
A
A
A
1
-4.44
0.50
120.30
115.86
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
77
77
77
N
1
-12.50
2.00
118.30
105.80
H
H
H
CG
CD
OE2
GLU
GLU
GLU
80
80
80
N
1
-10.44
1.70
113.30
102.86
H
H
H
CA
CB
CG
MET
MET
MET
84
84
84
N
1
-3.90
0.60
121.00
117.10
H
H
H
CB
CG
CD2
TYR
TYR
TYR
94
94
94
N
1
6.32
0.50
120.30
126.62
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
97
97
97
N
1
-7.77
0.50
120.30
112.53
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
97
97
97
N
1
-8.54
0.90
118.30
109.76
H
H
H
CB
CG
OD2
ASP
ASP
ASP
100
100
100
N
1
7.98
0.50
120.30
128.28
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
101
101
101
N
1
-7.20
0.50
120.30
113.10
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
101
101
101
N
1
-7.48
0.90
118.30
110.82
H
H
H
CB
CG
OD2
ASP
ASP
ASP
102
102
102
N
1
10.15
1.60
122.70
132.85
H
H
H
O
C
N
ALA
ALA
PHE
113
113
114
Y
1
13.26
2.20
113.40
126.66
H
H
H
CA
CB
CG
GLU
GLU
GLU
127
127
127
N
1
-5.45
0.60
121.00
115.55
H
H
H
CB
CG
CD2
TYR
TYR
TYR
134
134
134
N
1
-5.61
0.90
119.80
114.19
H
H
H
CD1
CE1
CZ
TYR
TYR
TYR
134
134
134
N
1
-7.81
0.50
120.30
112.49
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
137
137
137
N
1
5.16
0.50
120.30
125.46
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
137
137
137
N
1
-15.35
2.20
111.50
96.15
H
H
H
N
CA
CB
VAL
VAL
VAL
154
154
154
N
1
-12.52
1.90
111.40
98.88
H
H
H
CB
CA
C
VAL
VAL
VAL
157
157
157
N
1
4.50
0.50
120.30
124.80
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
173
173
173
N
1
-4.56
0.50
120.30
115.74
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
175
175
175
N
1
4.57
0.50
120.30
124.87
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
175
175
175
N
A
A
A
1
-5.54
0.60
121.00
115.46
H
H
H
CB
CG
CD1
TYR
TYR
TYR
184
184
184
N
B
C
C
1
-15.22
2.10
122.30
107.08
H
H
H
C
N
CA
GLU
GLY
GLY
186
186
186
Y
1
3.33
0.50
120.30
123.63
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
187
187
187
N
1
7.59
1.20
123.30
130.89
H
H
H
OE1
CD
OE2
GLU
GLU
GLU
192
192
192
N
1
-12.89
2.10
120.10
107.21
H
H
H
CA
C
O
SER
SER
SER
195
195
195
N
1
15.26
2.30
121.90
137.16
H
H
H
OD1
CG
ND2
ASN
ASN
ASN
205
205
205
N
1
7.25
0.90
118.30
125.55
H
H
H
CB
CG
OD2
ASP
ASP
ASP
221
221
221
N
A
A
A
1
9.11
1.40
123.60
132.71
H
H
H
CD
NE
CZ
ARG
ARG
ARG
221
221
221
N
1
8.56
1.40
123.60
132.16
H
H
H
CD
NE
CZ
ARG
ARG
ARG
233
233
233
N
1
8.59
0.50
120.30
128.89
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
233
233
233
N
1
-6.98
0.50
120.30
113.32
H
H
H
NE
CZ
NH2
ARG
ARG
ARG
233
233
233
N
1
10.12
1.50
110.90
121.02
H
H
H
CA
CB
CG1
VAL
VAL
VAL
241
241
241
N
1
-6.90
0.90
118.30
111.40
H
H
H
CB
CG
OD2
ASP
ASP
ASP
243
243
243
N
1
L
L
CZ
NH1
ARG
ARG
15
15
0.079
0.013
1.326
1.405
N
1
H
H
N
CA
GLY
GLY
219
219
0.093
0.015
1.456
1.549
N
1
H
H
O
O
HOH
HOH
434
434
1.85
1_555
2_555
G
1
L
PHE
1
172.89
-130.16
C
1
L
GLU
1
-106.22
-105.55
B
1
L
ALA
1
-156.58
-53.49
1
L
PHE
7
-128.58
-66.19
J
1
L
TYR
14
-93.90
32.74
L
1
L
ASP
14
45.08
132.07
1
H
SER
48
-160.78
-167.15
A
1
H
TYR
60
-157.20
80.24
1
H
HIS
71
-126.11
-62.84
1
H
ILE
79
-120.73
-62.52
1
H
LYS
87
-173.14
146.92
D
1
H
LYS
186
-176.39
133.19
1
H
SER
195
-49.28
151.75
0.114
0.114
2.3
7.0
15157
1
2.0
2.3
7.0
204
2653
14
0
2435
0.022
2.7
1.2
1.5
1.9
2.0
2.6
2.5
3.5
3.0
model building
X-PLOR
refinement
PROLSQ
refinement
X-PLOR
phasing
X-PLOR
ALPHA THROMBIN (E.C.3.4.21.5) COMPLEXED WITH HIRUGEN (N-ACETYLHIRUDIN 53 - 64 WITH SULFATO-TYR 63)
THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK-THROMBIN: CHANGES ACCOMPANYING ACTIVATION AND EXOSITE BINDING TO 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
24
HELX_P
L
GLU
14
A
GLU
30
1
H1
7
B
H
H
ASP
125
B
ASP
122
HELX_P
H
LEU
130
B
LEU
130
1
H2
9
H
GLU
164
B
GLU
169
HELX_P
H
ASP
170
B
ASP
175
1
H3
7
H
HIS
230
B
HIS
242
HELX_P
H
GLN
244
B
GLN
256
1
H4
15
disulf
2.045
L
CYS
1
A
SG
CYS
9
1_555
H
CYS
122
B
SG
CYS
119
1_555
disulf
2.032
H
CYS
42
B
SG
CYS
28
1_555
H
CYS
58
B
SG
CYS
44
1_555
disulf
2.000
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
covale
1.466
one
G
N-Glycosylation
H
ASN
60
B
ND2
ASN
53
1_555
H
NAG
400
D
C1
NAG
1_555
covale
1.336
both
I
GLU
62
C
C
GLU
8
1_555
I
TYS
63
C
N
TYS
9
1_555
covale
1.320
both
I
TYS
63
C
C
TYS
9
1_555
I
LEU
64
C
N
LEU
10
1_555
COMPLEX(SERINE PROTEINASE/INHIBITOR)
COMPLEX(SERINE PROTEINASE-INHIBITOR), COMPLEX(SERINE PROTEINASE-INHIBITOR) complex
H
SER
36
B
SER
22
A
1
H
PRO
37
B
PRO
23
-3.32
THRB_HUMAN
UNP
1
328
P00734
THRB_HUMAN
UNP
2
364
P00734
1HAH
PDB
3
1HAH
328
363
1HAH
1
15
P00734
L
1
9
36
364
622
1HAH
16
247
P00734
H
2
1
259
55
64
1HAH
55
64
1HAH
I
3
1
10
7
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
H
TRP
29
B
TRP
14
H
LYS
36
B
LYS
21
H
LEU
41
B
LEU
27
H
ILE
47
B
ILE
33
H
ARG
50
B
ARG
36
H
ALA
55
B
ALA
41
H
ARG
101
B
ARG
98
H
LYS
109
B
LYS
106
H
GLU
80
B
GLU
76
H
PRO
92
B
PRO
88
H
ASP
63
B
ASP
58
H
GLY
69
B
GLY
64
H
TRP
29
B
TRP
14
H
LYS
36
B
LYS
21
H
GLY
133
B
GLY
133
H
TRP
141
B
TRP
141
H
LEU
155
B
LEU
160
H
ILE
162
B
ILE
167
H
ASN
179
B
ASN
184
H
LYS
185
B
LYS
191
H
TYR
225
B
TYR
237
H
THR
229
B
THR
241
H
ILE
212
B
ILE
224
H
GLY
219
B
GLY
230
H
ARG
206
B
ARG
218
H
GLN
209
B
GLN
221
H
GLY
196
B
GLY
206
H
SER
203
B
SER
213
H
GLY
133
B
GLY
133
H
TRP
141
B
TRP
141
Unknown
3
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
5
C 1 2 1