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2A45
Asym. Unit
Info
Asym.Unit (128 KB)
Biol.Unit 1 (121 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THROMBIN AND THE CENTRAL "E" REGION OF FIBRIN
Authors
:
I. Pechik, J. Madrazo, G. L. Gilliland, L. Medved
Date
:
27 Jun 05 (Deposition) - 02 May 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.65
Chains
:
Asym. Unit : A,B,D,E,G,H,I,J,K,L
Biol. Unit 1: A,B,D,E,G,H,I,J,K,L (1x)
Keywords
:
Thrombin, Fibrin, Fragment E, Thrombin-Fibrin Complex, Coiled Coils, Disulfide Rings, Blood Clotting, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Pechik, S. Yakovlev, M. W. Mosesson, G. L. Gilliland, L. Medved
Structural Basis For Sequential Cleavage Of Fibrinopeptides Upon Fibrin Assembly.
Biochemistry V. 45 3588 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMIN... (0G6a)
1b: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMIN... (0G6b)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0G6
2
Ligand/Ion
D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
2
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS B:42 , HIS B:57 , CYS B:58 , TRP B:60D , ASN B:98 , LEU B:99 , ASP B:189 , ALA B:190 , CYS B:191 , GLU B:192 , GLY B:193 , SER B:195 , SER B:214 , TRP B:215 , GLY B:216 , GLY B:226
BINDING SITE FOR RESIDUE 0G6 B 1
2
AC2
SOFTWARE
PO4 E:2 , HIS E:57 , CYS E:58 , TYR E:60A , ASN E:98 , LEU E:99 , ILE E:174 , ALA E:190 , CYS E:191 , GLU E:192 , GLY E:193 , SER E:195 , SER E:214 , TRP E:215 , GLY E:216 , GLY E:219 , CYS E:220
BINDING SITE FOR RESIDUE 0G6 E 1
3
AC3
SOFTWARE
LEU B:41 , GLY B:193 , ARG D:15
BINDING SITE FOR RESIDUE PO4 B 248
4
AC4
SOFTWARE
0G6 E:1 , LEU E:41 , CYS E:42 , CYS E:58 , LYS E:60F
BINDING SITE FOR RESIDUE PO4 E 2
[
close Site info
]
SAPs(SNPs)/Variants
(13, 26)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_006714 (M32T, chain B/E, )
02: VAR_072721 (C36R, chain G/J, )
03: VAR_011782 (P37T, chain B/E, )
04: VAR_002398 (S47T, chain G/J, )
05: VAR_072724 (C65R, chain H/K, )
06: VAR_006715 (R67C, chain B/E, )
07: VAR_002406 (A68T, chain H/K, )
08: VAR_013091 (P70S, chain H/K, )
09: VAR_006716 (R73H, chain B/E, )
10: VAR_006717 (R101W, chain B/E, )
11: VAR_006718 (E146A, chain B/E, )
12: VAR_068913 (E164Q, chain B/E, )
13: VAR_006719 (G226V, chain B/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_006714
M
380
T
THRB_HUMAN
Disease (FA2D)
---
B/E
M
32
T
02
UniProt
VAR_072721
C
55
R
FIBA_HUMAN
Disease (CAFBN)
---
G/J
C
36
R
03
UniProt
VAR_011782
P
386
T
THRB_HUMAN
Polymorphism
5897
B/E
P
37
T
04
UniProt
VAR_002398
S
66
T
FIBA_HUMAN
Polymorphism
---
G/J
S
47
T
05
UniProt
VAR_072724
C
95
R
FIBB_HUMAN
Disease (CAFBN)
---
H/K
C
65
R
06
UniProt
VAR_006715
R
425
C
THRB_HUMAN
Disease (FA2D)
---
B/E
R
67
C
07
UniProt
VAR_002406
A
98
T
FIBB_HUMAN
Disease (DYSFIBRIN)
---
H/K
A
68
T
08
UniProt
VAR_013091
P
100
S
FIBB_HUMAN
Polymorphism
2227434
H/K
P
70
S
09
UniProt
VAR_006716
R
431
H
THRB_HUMAN
Disease (FA2D)
---
B/E
R
73
H
10
UniProt
VAR_006717
R
461
W
THRB_HUMAN
Disease (FA2D)
---
B/E
R
101
W
11
UniProt
VAR_006718
E
509
A
THRB_HUMAN
Disease (FA2D)
---
B/E
E
146
A
12
UniProt
VAR_068913
E
532
Q
THRB_HUMAN
Polymorphism
---
B/E
E
164
Q
13
UniProt
VAR_006719
G
601
V
THRB_HUMAN
Disease (FA2D)
---
B/E
G
226
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (B:16-243,E:16-243)
2: TRYPSIN_HIS (B:53-58,E:53-58)
3: TRYPSIN_SER (B:189-200,E:189-200)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
THRB_HUMAN
364-618
2
B:16-243
E:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
THRB_HUMAN
402-407
2
B:53-58
E:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
THRB_HUMAN
562-573
2
B:189-200
E:189-200
[
close PROSITE info
]
Exons
(13, 28)
Info
All Exons
Exon 1.2 (G:26-41 | J:26-41)
Exon 1.3 (G:42-73 | J:42-73)
Exon 2.2d (H:54-72 | K:54-72)
Exon 2.3b (H:73-105 | K:73-105)
Exon 3.8 (A:1D-1A | - | D:1D-1A | -)
Exon 3.9 (A:1A-15 | B:16-29 | D:1A-15 | E:16...)
Exon 3.10 (- | B:29-75 | - | E:29-75)
Exon 3.11b (- | B:75-129B | - | E:75-129B)
Exon 3.12 (- | B:129B-184 | - | E:129B-184)
Exon 3.13 (- | B:184-202 | - | E:184-202)
Exon 3.14c (- | B:203-246 (gaps) | - | E:203-2...)
Exon 4.2a (I:6-15 | L:2-15)
Exon 4.2d (I:16-45 | L:16-45)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4b
04: Boundary 2.1a/2.2d
05: Boundary 2.2d/2.3b
06: Boundary 2.3b/2.4b
07: Boundary 3.7b/3.8
08: Boundary 3.8/3.9
09: Boundary 3.9/3.10
10: Boundary 3.10/3.11b
11: Boundary 3.11b/3.12
12: Boundary 3.12/3.13
13: Boundary 3.13/3.14c
14: Boundary 3.14c/-
15: Boundary 4.1f/4.2a
16: Boundary 4.2a/4.2d
17: Boundary 4.2d/4.2g
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000302053
1a
ENSE00001909776
chr4:
155511918-155511786
133
FIBA_HUMAN
1-18
18
0
-
-
1.2
ENST00000302053
2
ENSE00001127292
chr4:
155510714-155510589
126
FIBA_HUMAN
19-60
42
2
G:26-41
J:26-41
16
16
1.3
ENST00000302053
3
ENSE00001127283
chr4:
155510128-155509945
184
FIBA_HUMAN
61-122
62
2
G:42-73
J:42-73
32
32
1.4b
ENST00000302053
4b
ENSE00001127274
chr4:
155508809-155508664
146
FIBA_HUMAN
122-170
49
0
-
-
1.5b
ENST00000302053
5b
ENSE00001127263
chr4:
155508070-155506690
1381
FIBA_HUMAN
171-631
461
0
-
-
1.6
ENST00000302053
6
ENSE00001210975
chr4:
155505985-155504278
1708
FIBA_HUMAN
631-866
236
0
-
-
2.1a
ENST00000302068
1a
ENSE00001171218
chr4:
155484108-155484284
177
FIBB_HUMAN
1-38
38
0
-
-
2.2d
ENST00000302068
2d
ENSE00001640255
chr4:
155486960-155487151
192
FIBB_HUMAN
39-102
64
2
H:54-72
K:54-72
19
19
2.3b
ENST00000302068
3b
ENSE00001645081
chr4:
155487641-155487824
184
FIBB_HUMAN
103-164
62
2
H:73-105
K:73-105
33
33
2.4b
ENST00000302068
4b
ENSE00001127321
chr4:
155488745-155488972
228
FIBB_HUMAN
164-240
77
0
-
-
2.5
ENST00000302068
5
ENSE00001127313
chr4:
155489533-155489646
114
FIBB_HUMAN
240-278
39
0
-
-
2.6
ENST00000302068
6
ENSE00001127308
chr4:
155490334-155490459
126
FIBB_HUMAN
278-320
43
0
-
-
2.7
ENST00000302068
7
ENSE00001127300
chr4:
155490666-155490951
286
FIBB_HUMAN
320-415
96
0
-
-
2.8c
ENST00000302068
8c
ENSE00001171210
chr4:
155491571-155492238
668
FIBB_HUMAN
415-491
77
0
-
-
3.1a
ENST00000311907
1a
ENSE00001931088
chr11:
46740730-46740864
135
THRB_HUMAN
1-27
27
0
-
-
3.2a
ENST00000311907
2a
ENSE00001181543
chr11:
46741252-46741412
161
THRB_HUMAN
27-80
54
0
-
-
3.3
ENST00000311907
3
ENSE00001181538
chr11:
46742073-46742097
25
THRB_HUMAN
81-89
9
0
-
-
3.4
ENST00000311907
4
ENSE00001181532
chr11:
46742340-46742390
51
THRB_HUMAN
89-106
18
0
-
-
3.6a
ENST00000311907
6a
ENSE00001181527
chr11:
46744730-46744835
106
THRB_HUMAN
106-141
36
0
-
-
3.6c
ENST00000311907
6c
ENSE00001181524
chr11:
46744932-46745068
137
THRB_HUMAN
141-187
47
0
-
-
3.7b
ENST00000311907
7b
ENSE00001688723
chr11:
46747409-46747723
315
THRB_HUMAN
187-292
106
0
-
-
3.8
ENST00000311907
8
ENSE00002179953
chr11:
46748048-46748176
129
THRB_HUMAN
292-335
44
2
A:1D-1A
-
D:1D-1A
-
4
-
4
-
3.9
ENST00000311907
9
ENSE00001770269
chr11:
46748261-46748387
127
THRB_HUMAN
335-377
43
4
A:1A-15
B:16-29
D:1A-15
E:16-29
29
14
29
14
3.10
ENST00000311907
10
ENSE00001650441
chr11:
46749546-46749713
168
THRB_HUMAN
377-433
57
2
-
B:29-75
-
E:29-75
-
57
-
57
3.11b
ENST00000311907
11b
ENSE00001657931
chr11:
46750214-46750387
174
THRB_HUMAN
433-491
59
2
-
B:75-129B
-
E:75-129B
-
59
-
59
3.12
ENST00000311907
12
ENSE00001646362
chr11:
46750930-46751111
182
THRB_HUMAN
491-552
62
2
-
B:129B-184
-
E:129B-184
-
62
-
62
3.13
ENST00000311907
13
ENSE00001680217
chr11:
46760598-46760668
71
THRB_HUMAN
552-575
24
2
-
B:184-202
-
E:184-202
-
24
-
24
3.14c
ENST00000311907
14c
ENSE00001227030
chr11:
46760815-46761056
242
THRB_HUMAN
576-622
47
2
-
B:203-246 (gaps)
-
E:203-246 (gaps)
-
47
-
47
4.1f
ENST00000336098
1f
ENSE00001820766
chr4:
155533800-155533684
117
FIBG_HUMAN
1-26
26
0
-
-
4.2a
ENST00000336098
2a
ENSE00001781463
chr4:
155533587-155533543
45
FIBG_HUMAN
27-41
15
2
I:6-15
L:2-15
10
14
4.2d
ENST00000336098
2d
ENSE00001624767
chr4:
155533353-155533170
184
FIBG_HUMAN
42-103
62
2
I:16-45
L:16-45
30
30
4.2g
ENST00000336098
2g
ENSE00001652916
chr4:
155533050-155532957
94
FIBG_HUMAN
103-134
32
0
-
-
4.3a
ENST00000336098
3a
ENSE00001127239
chr4:
155531349-155531219
131
FIBG_HUMAN
134-178
45
0
-
-
4.3f
ENST00000336098
3f
ENSE00002146570
chr4:
155530915-155530782
134
FIBG_HUMAN
178-222
45
0
-
-
4.4b
ENST00000336098
4b
ENSE00001127220
chr4:
155529802-155529618
185
FIBG_HUMAN
223-284
62
0
-
-
4.5
ENST00000336098
5
ENSE00001127212
chr4:
155528134-155527857
278
FIBG_HUMAN
284-377
94
0
-
-
4.6c
ENST00000336098
6c
ENSE00001344514
chr4:
155526218-155525728
491
FIBG_HUMAN
377-453
77
0
-
-
[
close EXON info
]
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d2a45_1 (A:,B:)
1b: SCOP_d2a45_2 (D:,E:)
2a: SCOP_d2a45g_ (G:)
2b: SCOP_d2a45j_ (J:)
3a: SCOP_d2a45h_ (H:)
3b: SCOP_d2a45k_ (K:)
4a: SCOP_d2a45i_ (I:)
4b: SCOP_d2a45l_ (L:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Thrombin
(188)
Human (Homo sapiens) [TaxId: 9606]
(169)
1a
d2a45.1
A:,B:
1b
d2a45.2
D:,E:
Class
:
Coiled coil proteins
(689)
Fold
:
Parallel coiled-coil
(407)
Superfamily
:
Fibrinogen coiled-coil and central regions
(71)
Family
:
Fibrinogen coiled-coil and central regions
(70)
Protein domain
:
Fibrinogen alpha chain
(27)
Human (Homo sapiens) [TaxId: 9606]
(22)
2a
d2a45g_
G:
2b
d2a45j_
J:
Protein domain
:
Fibrinogen beta chain
(20)
Human (Homo sapiens) [TaxId: 9606]
(15)
3a
d2a45h_
H:
3b
d2a45k_
K:
Protein domain
:
Fibrinogen gamma chain
(23)
Human (Homo sapiens) [TaxId: 9606]
(18)
4a
d2a45i_
I:
4b
d2a45l_
L:
[
close SCOP info
]
CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_2a45H00 (H:54-105)
1b: CATH_2a45K00 (K:54-105)
1c: CATH_2a45L00 (L:2-45)
1d: CATH_2a45I00 (I:6-45)
1e: CATH_2a45G00 (G:26-73)
1f: CATH_2a45J00 (J:26-73)
2a: CATH_2a45B02 (B:28-120,B:233-246)
2b: CATH_2a45B01 (B:16-27,B:121-232)
2c: CATH_2a45E01 (E:16-27,E:121-232)
2d: CATH_2a45E02 (E:28-120,E:233-246)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.50, no name defined]
(33)
Human (Homo sapiens)
(28)
1a
2a45H00
H:54-105
1b
2a45K00
K:54-105
1c
2a45L00
L:2-45
1d
2a45I00
I:6-45
1e
2a45G00
G:26-73
1f
2a45J00
J:26-73
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
2a
2a45B02
B:28-120,B:233-246
2b
2a45B01
B:16-27,B:121-232
2c
2a45E01
E:16-27,E:121-232
2d
2a45E02
E:28-120,E:233-246
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
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Nucleic
Backbone
Sidechain
Hetero
Ligand
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All Atoms
Protein & NOT Variant
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Protein & NOT PROSITE
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Chain B
Chain D
Chain E
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
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Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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