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1LWU
Biol. Unit 2
Info
Asym.Unit (509 KB)
Biol.Unit 1 (253 KB)
Biol.Unit 2 (254 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FRAGMENT D FROM LAMPREY FIBRINOGEN COMPLEXED WITH THE PEPTIDE GLY-HIS-ARG-PRO-AMIDE
Authors
:
Z. Yang, G. Spraggon, L. Pandi, S. J. Everse, M. Riley, R. F. Doolittle
Date
:
03 Jun 02 (Deposition) - 23 Aug 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,J,K,L,M,P (1x)
Biol. Unit 2: D,E,F,G,H,I,N,O (1x)
Keywords
:
Heterotrimer, Protein-Peptide Complex, Blood Clotting
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Yang, G. Spraggon, L. Pandi, S. J. Everse, M. Riley, R. F. Doolittle
Crystal Structure Of Fragment D From Lamprey Fibrinogen Complexed With The Peptide Gly-His-Arg-Pro-Amide.
Biochemistry V. 41 10218 2002
[
close entry info
]
Hetero Components
(6, 21)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
3a: BETA-D-GALACTOSE (GALa)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
4g: ALPHA-D-MANNOSE (MANg)
4h: ALPHA-D-MANNOSE (MANh)
4i: ALPHA-D-MANNOSE (MANi)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
6b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
6c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
6d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
6e: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGe)
6f: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGf)
6g: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGg)
6h: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGh)
7a: AMINO GROUP (NH2a)
7b: AMINO GROUP (NH2b)
7c: AMINO GROUP (NH2c)
7d: AMINO GROUP (NH2d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NDG
5
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7
NH2
2
Mod. Amino Acid
AMINO GROUP
[
close Hetero Component info
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Sites
(27, 27)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
12: BC5 (SOFTWARE)
13: BC6 (SOFTWARE)
14: BC7 (SOFTWARE)
15: BC9 (SOFTWARE)
16: CC2 (SOFTWARE)
17: CC4 (SOFTWARE)
18: CC5 (SOFTWARE)
19: CC6 (SOFTWARE)
20: CC7 (SOFTWARE)
21: CC8 (SOFTWARE)
22: CC9 (SOFTWARE)
23: DC4 (SOFTWARE)
24: DC6 (SOFTWARE)
25: DC7 (SOFTWARE)
26: EC1 (SOFTWARE)
27: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET B:381 , ASN B:384 , GLY E:339 , NDG M:571
BINDING SITE FOR RESIDUE NDG B 570
02
AC3
SOFTWARE
MET E:381 , ASN E:384 , NDG N:571
BINDING SITE FOR RESIDUE NAG E 570
03
AC5
SOFTWARE
NAG E:570 , BMA E:572 , MAN N:576
BINDING SITE FOR RESIDUE NDG N 571
04
AC6
SOFTWARE
BMA E:573 , NDG N:571 , MAN N:576
BINDING SITE FOR RESIDUE BMA E 572
05
AC7
SOFTWARE
MET H:381 , ASN H:384 , HIS O:2 , PRO O:4 , NDG O:571
BINDING SITE FOR RESIDUE NDG H 570
06
AC8
SOFTWARE
HIS B:266 , NDG D:574 , BMA E:572
BINDING SITE FOR RESIDUE BMA E 573
07
AC9
SOFTWARE
MAN H:480 , NDG K:570
BINDING SITE FOR RESIDUE NDG H 571
08
BC1
SOFTWARE
HIS B:266 , GLY B:267 , BMA E:573
BINDING SITE FOR RESIDUE NDG D 574
09
BC2
SOFTWARE
NDG H:571 , MAN H:573 , MAN P:576
BINDING SITE FOR RESIDUE MAN H 480
10
BC3
SOFTWARE
BMA E:572 , NDG N:571
BINDING SITE FOR RESIDUE MAN N 576
11
BC4
SOFTWARE
NDG H:571 , ASN K:384 , HIS P:2
BINDING SITE FOR RESIDUE NDG K 570
12
BC5
SOFTWARE
NDG H:570 , BMA H:572
BINDING SITE FOR RESIDUE NDG O 571
13
BC6
SOFTWARE
NDG O:571
BINDING SITE FOR RESIDUE BMA H 572
14
BC7
SOFTWARE
HIS H:266 , MAN H:480 , NAG H:574
BINDING SITE FOR RESIDUE MAN H 573
15
BC9
SOFTWARE
HIS H:266 , GLY H:267 , MAN H:573 , GAL H:575
BINDING SITE FOR RESIDUE NAG H 574
16
CC2
SOFTWARE
NAG H:574
BINDING SITE FOR RESIDUE GAL H 575
17
CC4
SOFTWARE
MAN H:480
BINDING SITE FOR RESIDUE MAN P 576
18
CC5
SOFTWARE
ASN F:203 , NAG F:571
BINDING SITE FOR RESIDUE NAG F 570
19
CC6
SOFTWARE
NAG F:570 , MAN F:572
BINDING SITE FOR RESIDUE NAG F 571
20
CC7
SOFTWARE
NAG F:571
BINDING SITE FOR RESIDUE MAN F 572
21
CC8
SOFTWARE
ASN I:203 , THR I:205 , NAG I:571
BINDING SITE FOR RESIDUE NAG I 570
22
CC9
SOFTWARE
NAG I:570 , MAN J:572
BINDING SITE FOR RESIDUE NAG I 571
23
DC4
SOFTWARE
NAG I:571
BINDING SITE FOR RESIDUE MAN J 572
24
DC6
SOFTWARE
ASP E:401 , ASP E:403 , TRP E:405 , LYS E:412
BINDING SITE FOR RESIDUE CA E 2
25
DC7
SOFTWARE
ASP H:401 , ASP H:403 , TRP H:405 , LYS H:412
BINDING SITE FOR RESIDUE CA H 3
26
EC1
SOFTWARE
ASP F:316 , ASP F:318 , TYR F:320 , GLY F:322
BINDING SITE FOR RESIDUE CA F 6
27
EC2
SOFTWARE
ASP I:316 , ASP I:318 , TYR I:320 , GLY I:322
BINDING SITE FOR RESIDUE CA I 7
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: FIBRINOGEN_C_2 (F:145-388,I:145-388)
2: FIBRINOGEN_C_1 (F:332-344,I:332-344)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FIBRINOGEN_C_2
PS51406
Fibrinogen C-terminal domain profile.
FIBG_PETMA
169-412
2
-
F:145-388
I:145-388
-
FIBB_PETMA
221-476
2
-
E:223-477
H:223-477
-
2
FIBRINOGEN_C_1
PS00514
Fibrinogen C-terminal domain signature.
FIBG_PETMA
356-368
2
-
F:332-344
I:332-344
-
FIBB_PETMA
420-432
2
-
E:422-434
H:422-434
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 20)
Info
All SCOP Domains
1a: SCOP_d1lwub1 (B:219-477)
1b: SCOP_d1lwue1 (E:219-477)
1c: SCOP_d1lwuh1 (H:219-477)
1d: SCOP_d1lwuk1 (K:219-477)
2a: SCOP_d1lwuc1 (C:138-399)
2b: SCOP_d1lwuf1 (F:138-399)
2c: SCOP_d1lwui1 (I:138-395)
2d: SCOP_d1lwul1 (L:138-395)
3a: SCOP_d1lwua_ (A:)
3b: SCOP_d1lwud_ (D:)
3c: SCOP_d1lwug_ (G:)
3d: SCOP_d1lwuj_ (J:)
4a: SCOP_d1lwub2 (B:163-218)
4b: SCOP_d1lwue2 (E:163-218)
4c: SCOP_d1lwuh2 (H:163-218)
4d: SCOP_d1lwuk2 (K:163-218)
5a: SCOP_d1lwuc2 (C:83-137)
5b: SCOP_d1lwuf2 (F:83-137)
5c: SCOP_d1lwui2 (I:83-137)
5d: SCOP_d1lwul2 (L:83-137)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Fibrinogen C-terminal domain-like
(70)
Superfamily
:
Fibrinogen C-terminal domain-like
(70)
Family
:
Fibrinogen C-terminal domain-like
(43)
Protein domain
:
Fibrinogen C-terminal domains
(42)
Sea lamprey (Petromyzon marinus), beta [TaxId: 7757]
(2)
1a
d1lwub1
B:219-477
1b
d1lwue1
E:219-477
1c
d1lwuh1
H:219-477
1d
d1lwuk1
K:219-477
Sea lamprey (Petromyzon marinus), gamma [TaxId: 7757]
(2)
2a
d1lwuc1
C:138-399
2b
d1lwuf1
F:138-399
2c
d1lwui1
I:138-395
2d
d1lwul1
L:138-395
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)
Sea lamprey (Petromyzon marinus) [TaxId: 7757]
(2)
3a
d1lwua_
A:
3b
d1lwud_
D:
3c
d1lwug_
G:
3d
d1lwuj_
J:
Protein domain
:
Fibrinogen beta chain
(20)
Sea lamprey (Petromyzon marinus) [TaxId: 7757]
(2)
4a
d1lwub2
B:163-218
4b
d1lwue2
E:163-218
4c
d1lwuh2
H:163-218
4d
d1lwuk2
K:163-218
Protein domain
:
Fibrinogen gamma chain
(23)
Sea lamprey (Petromyzon marinus) [TaxId: 7757]
(2)
5a
d1lwuc2
C:83-137
5b
d1lwuf2
F:83-137
5c
d1lwui2
I:83-137
5d
d1lwul2
L:83-137
[
close SCOP info
]
CATH Domains
(3, 28)
Info
all CATH domains
1a: CATH_1lwuC01 (C:145-284,C:379-389)
1b: CATH_1lwuF01 (F:145-284,F:379-389)
1c: CATH_1lwuI01 (I:145-284,I:379-389)
1d: CATH_1lwuL01 (L:145-284,L:379-389)
1e: CATH_1lwuB01 (B:223-369,B:469-477)
1f: CATH_1lwuE01 (E:223-369,E:469-477)
1g: CATH_1lwuH01 (H:223-369,H:469-477)
1h: CATH_1lwuK01 (K:223-369,K:469-477)
2a: CATH_1lwuC02 (C:285-378)
2b: CATH_1lwuF02 (F:285-378)
2c: CATH_1lwuI02 (I:285-378)
2d: CATH_1lwuL02 (L:285-378)
2e: CATH_1lwuB02 (B:370-468)
2f: CATH_1lwuE02 (E:370-468)
2g: CATH_1lwuH02 (H:370-468)
2h: CATH_1lwuK02 (K:370-468)
3a: CATH_1lwuC03 (C:83-144)
3b: CATH_1lwuF03 (F:83-144)
3c: CATH_1lwuA00 (A:95-193)
3d: CATH_1lwuD00 (D:95-193)
3e: CATH_1lwuG00 (G:95-193)
3f: CATH_1lwuJ00 (J:95-193)
3g: CATH_1lwuI03 (I:83-144)
3h: CATH_1lwuL03 (L:83-144)
3i: CATH_1lwuB03 (B:163-222)
3j: CATH_1lwuE03 (E:163-222)
3k: CATH_1lwuH03 (H:163-222)
3l: CATH_1lwuK03 (K:163-222)
View:
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(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Gamma Fibrinogen; Chain A, domain 1
(58)
Homologous Superfamily
:
Gamma Fibrinogen, chain A, domain 1
(58)
Sea lamprey (Petromyzon marinus)
(2)
1a
1lwuC01
C:145-284,C:379-389
1b
1lwuF01
F:145-284,F:379-389
1c
1lwuI01
I:145-284,I:379-389
1d
1lwuL01
L:145-284,L:379-389
1e
1lwuB01
B:223-369,B:469-477
1f
1lwuE01
E:223-369,E:469-477
1g
1lwuH01
H:223-369,H:469-477
1h
1lwuK01
K:223-369,K:469-477
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
(58)
Homologous Superfamily
:
Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
(58)
Sea lamprey (Petromyzon marinus)
(2)
2a
1lwuC02
C:285-378
2b
1lwuF02
F:285-378
2c
1lwuI02
I:285-378
2d
1lwuL02
L:285-378
2e
1lwuB02
B:370-468
2f
1lwuE02
E:370-468
2g
1lwuH02
H:370-468
2h
1lwuK02
K:370-468
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)
Sea lamprey (Petromyzon marinus)
(2)
3a
1lwuC03
C:83-144
3b
1lwuF03
F:83-144
3c
1lwuA00
A:95-193
3d
1lwuD00
D:95-193
3e
1lwuG00
G:95-193
3f
1lwuJ00
J:95-193
3g
1lwuI03
I:83-144
3h
1lwuL03
L:83-144
3i
1lwuB03
B:163-222
3j
1lwuE03
E:163-222
3k
1lwuH03
H:163-222
3l
1lwuK03
K:163-222
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Fibrinogen_C_1lwuL01 (L:150-387)
1b: PFAM_Fibrinogen_C_1lwuL02 (L:150-387)
1c: PFAM_Fibrinogen_C_1lwuL03 (L:150-387)
1d: PFAM_Fibrinogen_C_1lwuL04 (L:150-387)
2a: PFAM_Fib_alpha_1lwuJ01 (J:95-167)
2b: PFAM_Fib_alpha_1lwuJ02 (J:95-167)
2c: PFAM_Fib_alpha_1lwuJ03 (J:95-167)
2d: PFAM_Fib_alpha_1lwuJ04 (J:95-167)
2e: PFAM_Fib_alpha_1lwuL05 (L:83-148)
2f: PFAM_Fib_alpha_1lwuL06 (L:83-148)
2g: PFAM_Fib_alpha_1lwuL07 (L:83-148)
2h: PFAM_Fib_alpha_1lwuL08 (L:83-148)
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Clans
(
)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Fibrinogen_C
(23)
Family
:
Fibrinogen_C
(23)
Petromyzon marinus (Sea lamprey)
(2)
1a
Fibrinogen_C-1lwuL01
L:150-387
1b
Fibrinogen_C-1lwuL02
L:150-387
1c
Fibrinogen_C-1lwuL03
L:150-387
1d
Fibrinogen_C-1lwuL04
L:150-387
Clan
:
no clan defined [family: Fib_alpha]
(17)
Family
:
Fib_alpha
(17)
Petromyzon marinus (Sea lamprey)
(2)
2a
Fib_alpha-1lwuJ01
J:95-167
2b
Fib_alpha-1lwuJ02
J:95-167
2c
Fib_alpha-1lwuJ03
J:95-167
2d
Fib_alpha-1lwuJ04
J:95-167
2e
Fib_alpha-1lwuL05
L:83-148
2f
Fib_alpha-1lwuL06
L:83-148
2g
Fib_alpha-1lwuL07
L:83-148
2h
Fib_alpha-1lwuL08
L:83-148
[
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Atom Selection
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Nucleic
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Protein & NOT Variant
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Chain O
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (509 KB)
Header - Asym.Unit
Biol.Unit 1 (253 KB)
Header - Biol.Unit 1
Biol.Unit 2 (254 KB)
Header - Biol.Unit 2
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