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Asym. Unit
Info
Asym.Unit (238 KB)
Biol.Unit 1 (233 KB)
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(1)
Title
:
HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE
Authors
:
B. A. Fox, V. C. Yee, L. C. Pederson, I. Le Trong, P. D. Bishop, R. E. Stenkamp, D. C. Teller
Date
:
14 Jun 99 (Deposition) - 02 Jul 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transglutaminase, Blood Coagulation, Calcium, Strontium, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. A. Fox, V. C. Yee, L. C. Pedersen, I. Le Trong, P. D. Bishop, R. E. Stenkamp, D. C. Teller
Identification Of The Calcium Binding Site And A Novel Ytterbium Site In Blood Coagulation Factor Xiii By X-Ray Crystallography.
J. Biol. Chem. V. 274 4917 1999
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: STRONTIUM ION (SRa)
1b: STRONTIUM ION (SRb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SR
2
Ligand/Ion
STRONTIUM ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: CAT (AUTHOR)
4: CBT (AUTHOR)
5: INA (AUTHOR)
6: INB (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:457 , GLU A:485
BINDING SITE FOR RESIDUE SR A 732
2
AC2
SOFTWARE
ASN B:436 , ALA B:457 , GLU B:485
BINDING SITE FOR RESIDUE SR B 732
3
CAT
AUTHOR
CYS A:314 , HIS A:373 , ASP A:396
CATALYTIC TRIAD IN CHAIN A
4
CBT
AUTHOR
CYS B:314 , HIS B:373 , ASP B:396
CATALYTIC TRIAD IN CHAIN B
5
INA
AUTHOR
ALA A:457 , ASN A:436 , GLU A:485 , GLU A:490
ION BINDING SITE A STRONTIUM LIGANDS
6
INB
AUTHOR
ALA B:457 , ASN B:436 , GLU B:485 , GLU B:490
ION BINDING SITE B STRONTIUM LIGANDS
[
close Site info
]
SAPs(SNPs)/Variants
(10, 19)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_013927 (V34L, chain B, )
02: VAR_020911 (Y204F, chain A/B, )
03: VAR_057350 (M350K, chain A/B, )
04: VAR_013928 (T550I, chain A/B, )
05: VAR_007471 (P564L, chain A/B, )
06: VAR_013929 (L588Q, chain A/B, )
07: VAR_060545 (T649I, chain A/B, )
08: VAR_007472 (V650I, chain A/B, )
09: VAR_007473 (E651E, chain A/B, )
10: VAR_007474 (R681H, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_013927
V
35
L
F13A_HUMAN
Polymorphism
5985
B
V
34
L
02
UniProt
VAR_020911
Y
205
F
F13A_HUMAN
Polymorphism
3024477
A/B
Y
204
F
03
UniProt
VAR_057350
M
351
K
F13A_HUMAN
Polymorphism
2230848
A/B
M
350
K
04
UniProt
VAR_013928
T
551
I
F13A_HUMAN
Polymorphism
5984
A/B
T
550
I
05
UniProt
VAR_007471
P
565
L
F13A_HUMAN
Polymorphism
5982
A/B
P
564
L
06
UniProt
VAR_013929
L
589
Q
F13A_HUMAN
Polymorphism
5983
A/B
L
588
Q
07
UniProt
VAR_060545
T
650
I
F13A_HUMAN
Polymorphism
17852475
A/B
T
649
I
08
UniProt
VAR_007472
V
651
I
F13A_HUMAN
Polymorphism
5987
A/B
V
650
I
09
UniProt
VAR_007473
Q
652
E
F13A_HUMAN
Polymorphism
5988
A/B
E
651
E
10
UniProt
VAR_007474
R
682
H
F13A_HUMAN
Disease (FA13AD)
---
A/B
R
681
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: TRANSGLUTAMINASES (A:312-329,B:312-329)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRANSGLUTAMINASES
PS00547
Transglutaminases active site.
F13A_HUMAN
313-330
2
A:312-329
B:312-329
[
close PROSITE info
]
Exons
(14, 28)
Info
All Exons
Exon 1.3 (A:9-30 | B:10-43 (gaps))
Exon 1.4b (A:45-106 | B:43-106)
Exon 1.5c (A:106-190 | B:106-190)
Exon 1.6b (A:190-229 | B:190-229)
Exon 1.7 (A:230-265 | B:230-265)
Exon 1.8a (A:266-324 | B:266-324)
Exon 1.9 (A:324-370 | B:324-370)
Exon 1.11 (A:370-405 | B:370-405)
Exon 1.12 (A:405-434 | B:405-434)
Exon 1.13 (A:435-486 | B:435-486)
Exon 1.14 (A:486-582 (gaps) | B:486-582 (gaps...)
Exon 1.15 (A:582-635 | B:582-635)
Exon 1.16 (A:636-681 | B:636-681)
Exon 1.17 (A:681-727 | B:681-727)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2b/1.3
02: Boundary 1.3/1.4b
03: Boundary 1.4b/1.5c
04: Boundary 1.5c/1.6b
05: Boundary 1.6b/1.7
06: Boundary 1.7/1.8a
07: Boundary 1.8a/1.9
08: Boundary 1.9/1.11
09: Boundary 1.11/1.12
10: Boundary 1.12/1.13
11: Boundary 1.13/1.14
12: Boundary 1.14/1.15
13: Boundary 1.15/1.16
14: Boundary 1.16/1.17
15: Boundary 1.17/-
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
1.2b
ENST00000264870
2b
ENSE00001855494
chr6:
6321067-6320820
248
F13A_HUMAN
-
0
0
-
-
1.3
ENST00000264870
3
ENSE00002201786
chr6:
6318915-6318768
148
F13A_HUMAN
1-44
44
2
A:9-30
B:10-43 (gaps)
22
34
1.4b
ENST00000264870
4b
ENSE00001972641
chr6:
6305772-6305584
189
F13A_HUMAN
44-107
64
2
A:45-106
B:43-106
62
64
1.5c
ENST00000264870
5c
ENSE00002191677
chr6:
6267042-6266791
252
F13A_HUMAN
107-191
85
2
A:106-190
B:106-190
85
85
1.6b
ENST00000264870
6b
ENSE00001969635
chr6:
6251162-6251044
119
F13A_HUMAN
191-230
40
2
A:190-229
B:190-229
40
40
1.7
ENST00000264870
7
ENSE00001967644
chr6:
6248652-6248545
108
F13A_HUMAN
231-266
36
2
A:230-265
B:230-265
36
36
1.8a
ENST00000264870
8a
ENSE00001984690
chr6:
6225093-6224919
175
F13A_HUMAN
267-325
59
2
A:266-324
B:266-324
59
59
1.9
ENST00000264870
9
ENSE00001959052
chr6:
6222404-6222266
139
F13A_HUMAN
325-371
47
2
A:324-370
B:324-370
47
47
1.11
ENST00000264870
11
ENSE00001971321
chr6:
6197559-6197456
104
F13A_HUMAN
371-406
36
2
A:370-405
B:370-405
36
36
1.12
ENST00000264870
12
ENSE00001981205
chr6:
6196118-6196030
89
F13A_HUMAN
406-435
30
2
A:405-434
B:405-434
30
30
1.13
ENST00000264870
13
ENSE00001990320
chr6:
6182374-6182221
154
F13A_HUMAN
436-487
52
2
A:435-486
B:435-486
52
52
1.14
ENST00000264870
14
ENSE00001984164
chr6:
6175100-6174813
288
F13A_HUMAN
487-583
97
2
A:486-582 (gaps)
B:486-582 (gaps)
97
97
1.15
ENST00000264870
15
ENSE00001989225
chr6:
6167851-6167691
161
F13A_HUMAN
583-636
54
2
A:582-635
B:582-635
54
54
1.16
ENST00000264870
16
ENSE00001973719
chr6:
6152182-6152046
137
F13A_HUMAN
637-682
46
2
A:636-681
B:636-681
46
46
1.17
ENST00000264870
17
ENSE00001603521
chr6:
6146005-6144318
1688
F13A_HUMAN
682-732
51
2
A:681-727
B:681-727
47
47
[
close EXON info
]
SCOP Domains
(3, 8)
Info
All SCOP Domains
1a: SCOP_d1qrka1 (A:9-190)
1b: SCOP_d1qrkb1 (B:10-190)
2a: SCOP_d1qrka2 (A:517-627)
2b: SCOP_d1qrka3 (A:628-727)
2c: SCOP_d1qrkb2 (B:516-627)
2d: SCOP_d1qrkb3 (B:628-727)
3a: SCOP_d1qrka4 (A:191-511)
3b: SCOP_d1qrkb4 (B:191-507)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
Transglutaminase N-terminal domain
(17)
Protein domain
:
Transglutaminase N-terminal domain
(17)
Human (Homo sapiens), blood isozyme [TaxId: 9606]
(8)
1a
d1qrka1
A:9-190
1b
d1qrkb1
B:10-190
Superfamily
:
Transglutaminase, two C-terminal domains
(18)
Family
:
Transglutaminase, two C-terminal domains
(17)
Protein domain
:
Transglutaminase, two C-terminal domains
(17)
Human (Homo sapiens), blood isozyme [TaxId: 9606]
(8)
2a
d1qrka2
A:517-627
2b
d1qrka3
A:628-727
2c
d1qrkb2
B:516-627
2d
d1qrkb3
B:628-727
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Transglutaminase core
(22)
Protein domain
:
Transglutaminase catalytic domain
(17)
Human (Homo sapiens), blood isozyme [TaxId: 9606]
(8)
3a
d1qrka4
A:191-511
3b
d1qrkb4
B:191-507
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1qrkA02 (A:193-517)
1b: CATH_1qrkB02 (B:193-516)
2a: CATH_1qrkA03 (A:518-630)
2b: CATH_1qrkB03 (B:517-630)
2c: CATH_1qrkA04 (A:631-724)
2d: CATH_1qrkB04 (B:631-724)
2e: CATH_1qrkA01 (A:9-192)
2f: CATH_1qrkB01 (B:10-192)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Coagulation Factor XIII; Chain A, domain 2
(19)
Homologous Superfamily
:
Coagulation Factor XIII, subunit A, domain 2
(19)
Human (Homo sapiens)
(18)
1a
1qrkA02
A:193-517
1b
1qrkB02
B:193-516
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1qrkA03
A:518-630
2b
1qrkB03
B:517-630
2c
1qrkA04
A:631-724
2d
1qrkB04
B:631-724
2e
1qrkA01
A:9-192
2f
1qrkB01
B:10-192
[
close CATH info
]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_Transglut_C_1qrkB01 (B:630-727)
1b: PFAM_Transglut_C_1qrkB02 (B:630-727)
1c: PFAM_Transglut_C_1qrkB03 (B:630-727)
1d: PFAM_Transglut_C_1qrkB04 (B:630-727)
2a: PFAM_Transglut_core_1qrkB05 (B:281-397)
2b: PFAM_Transglut_core_1qrkB06 (B:281-397)
3a: PFAM_Transglut_N_1qrkB07 (B:45-166)
3b: PFAM_Transglut_N_1qrkB08 (B:45-166)
View:
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
E-set
(290)
Family
:
Transglut_C
(8)
Homo sapiens (Human)
(8)
1a
Transglut_C-1qrkB01
B:630-727
1b
Transglut_C-1qrkB02
B:630-727
1c
Transglut_C-1qrkB03
B:630-727
1d
Transglut_C-1qrkB04
B:630-727
Clan
:
Peptidase_CA
(169)
Family
:
Transglut_core
(7)
Homo sapiens (Human)
(7)
2a
Transglut_core-1qrkB05
B:281-397
2b
Transglut_core-1qrkB06
B:281-397
Clan
:
no clan defined [family: Transglut_N]
(7)
Family
:
Transglut_N
(7)
Homo sapiens (Human)
(7)
3a
Transglut_N-1qrkB07
B:45-166
3b
Transglut_N-1qrkB08
B:45-166
[
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