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2QQK
Asym. Unit
Info
Asym.Unit (162 KB)
Biol.Unit 1 (307 KB)
Biol.Unit 2 (155 KB)
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(1)
Title
:
NEUROPILIN-2 A1A2B1B2 DOMAINS IN COMPLEX WITH A SEMAPHORIN-BLOCKING FAB
Authors
:
B. A. Appleton, C. Wiesmann
Date
:
26 Jul 07 (Deposition) - 20 Nov 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,H,L
Biol. Unit 1: A,H,L (2x)
Biol. Unit 2: A,H,L (1x)
Keywords
:
Vegf Receptor, Semaphorin Receptor, Phage-Derived Antibody, Developmental Protein, Differentiation, Glycoprotein, Membrane, Neurogenesis, Transmembrane, Hormone, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. A. Appleton, P. Wu, J. Maloney, J. Yin, W. C. Liang, S. Stawicki, K. Mortara, K. K. Bowman, J. M. Elliott, W. Desmarais, J. F. Bazan, A. Bagri, M. Tessier-Lavigne, A. W. Koch, Y. Wu, R. J. Watts, C. Wiesman
Structural Studies Of Neuropilin/Antibody Complexes Provide Insights Into Semaphorin And Vegf Binding
Embo J. V. 26 4902 2007
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:150 , ASN A:152
BINDING SITE FOR RESIDUE NAG A 1
2
AC2
SOFTWARE
ASN A:157
BINDING SITE FOR RESIDUE NAG A 602
[
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]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_047754 (K123K, chain A, )
2: VAR_066403 (W148R, chain L, )
3: VAR_003897 (V191L, chain L, )
4: VAR_067537 (R334C, chain A, )
5: VAR_067538 (R428W, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_047754
R
123
K
NRP2_HUMAN
Polymorphism
849541
A
K
123
K
2
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
L
W
148
R
3
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
L
V
191
L
4
UniProt
VAR_067537
R
334
C
NRP2_HUMAN
Polymorphism
114144673
A
R
334
C
5
UniProt
VAR_067538
R
428
W
NRP2_HUMAN
Polymorphism
139711818
A
R
428
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(5, 9)
Info
All PROSITE Patterns/Profiles
1: CUB (A:28-142|A:149-267)
2: IG_MHC (L:192-198)
3: FA58C_3 (A:277-427|A:434-592)
4: FA58C_1 (A:317-346|A:473-505)
5: FA58C_2 (A:411-427|A:575-592)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CUB
PS01180
CUB domain profile.
NRP2_HUMAN
28-142
149-267
2
A:28-142
A:149-267
2
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_HUMAN
85-91
1
L:192-198
3
FA58C_3
PS50022
Coagulation factors 5/8 type C domain (FA58C) profile.
NRP2_HUMAN
277-427
434-592
2
A:277-427
A:434-592
4
FA58C_1
PS01285
Coagulation factors 5/8 type C domain (FA58C) signature 1.
NRP2_HUMAN
317-346
473-505
2
A:317-346
A:473-505
5
FA58C_2
PS01286
Coagulation factors 5/8 type C domain (FA58C) signature 2.
NRP2_HUMAN
411-427
575-592
2
A:411-427
A:575-592
[
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]
Exons
(9, 9)
Info
All Exons
Exon 1.4a (A:27-84)
Exon 1.6b (A:84-145 (gaps))
Exon 1.7b (A:145-222 (gaps))
Exon 1.8b (A:222-274)
Exon 1.9 (A:274-330)
Exon 1.10 (A:331-382)
Exon 1.12 (A:383-431)
Exon 1.13a (A:431-547 (gaps))
Exon 1.14 (A:548-594)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2a/1.4a
02: Boundary 1.4a/1.6b
03: Boundary 1.6b/1.7b
04: Boundary 1.7b/1.8b
05: Boundary 1.8b/1.9
06: Boundary 1.9/1.10
07: Boundary 1.10/1.12
08: Boundary 1.12/1.13a
09: Boundary 1.13a/1.14
10: Boundary 1.14/1.15b
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
1.2a
ENST00000360409
2a
ENSE00001350724
chr2:
206547224-206548087
864
NRP2_HUMAN
1-25
25
0
-
-
1.4a
ENST00000360409
4a
ENSE00000796618
chr2:
206562268-206562445
178
NRP2_HUMAN
25-84
60
1
A:27-84
58
1.6b
ENST00000360409
6b
ENSE00000796621
chr2:
206580917-206581098
182
NRP2_HUMAN
84-145
62
1
A:84-145 (gaps)
62
1.7b
ENST00000360409
7b
ENSE00000796622
chr2:
206587202-206587432
231
NRP2_HUMAN
145-222
78
1
A:145-222 (gaps)
78
1.8b
ENST00000360409
8b
ENSE00000796624
chr2:
206588509-206588664
156
NRP2_HUMAN
222-274
53
1
A:222-274
53
1.9
ENST00000360409
9
ENSE00000796626
chr2:
206590637-206590806
170
NRP2_HUMAN
274-330
57
1
A:274-330
57
1.10
ENST00000360409
10
ENSE00000796629
chr2:
206592615-206592770
156
NRP2_HUMAN
331-382
52
1
A:331-382
52
1.12
ENST00000360409
12
ENSE00000796630
chr2:
206605243-206605387
145
NRP2_HUMAN
383-431
49
1
A:383-431
49
1.13a
ENST00000360409
13a
ENSE00001238400
chr2:
206607927-206608276
350
NRP2_HUMAN
431-547
117
1
A:431-547 (gaps)
117
1.14
ENST00000360409
14
ENSE00000796635
chr2:
206610470-206610614
145
NRP2_HUMAN
548-596
49
1
A:548-594
47
1.15b
ENST00000360409
15b
ENSE00000796636
chr2:
206614449-206614565
117
NRP2_HUMAN
596-635
40
0
-
-
1.16b
ENST00000360409
16b
ENSE00000796638
chr2:
206617559-206617699
141
NRP2_HUMAN
635-682
48
0
-
-
1.17c
ENST00000360409
17c
ENSE00000796640
chr2:
206628398-206628660
263
NRP2_HUMAN
682-769
88
0
-
-
1.19
ENST00000360409
19
ENSE00000796643
chr2:
206630198-206630294
97
NRP2_HUMAN
770-802
33
0
-
-
1.20b
ENST00000360409
20b
ENSE00001238223
chr2:
206631507-206631542
36
NRP2_HUMAN
802-814
13
0
-
-
1.23
ENST00000360409
23
ENSE00000796649
chr2:
206656959-206657009
51
NRP2_HUMAN
814-831
18
0
-
-
1.24d
ENST00000360409
24d
ENSE00001350546
chr2:
206659478-206662857
3380
NRP2_HUMAN
831-931
101
0
-
-
[
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]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2qqkl1 (L:1-107)
2a: SCOP_d2qqkl2 (L:108-211)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
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Superfamilies
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d2qqkl1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d2qqkl2
L:108-211
[
close SCOP info
]
CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_2qqkL02 (L:109-211)
1b: CATH_2qqkH02 (H:114-220)
1c: CATH_2qqkH01 (H:1-113)
1d: CATH_2qqkL01 (L:1-108)
2a: CATH_2qqkA02 (A:147-274)
2b: CATH_2qqkA01 (A:27-146)
3a: CATH_2qqkA04 (A:432-594)
3b: CATH_2qqkA03 (A:275-431)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
2qqkL02
L:109-211
1b
2qqkH02
H:114-220
1c
2qqkH01
H:1-113
1d
2qqkL01
L:1-108
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.290, no name defined]
(10)
Human (Homo sapiens)
(7)
2a
2qqkA02
A:147-274
2b
2qqkA01
A:27-146
Homologous Superfamily
:
Galactose-binding domain-like
(195)
Human (Homo sapiens)
(39)
3a
2qqkA04
A:432-594
3b
2qqkA03
A:275-431
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_CUB_2qqkA01 (A:149-264)
1b: PFAM_CUB_2qqkA02 (A:149-264)
2a: PFAM_F5_F8_type_C_2qqkA03 (A:449-589)
2b: PFAM_F5_F8_type_C_2qqkA04 (A:449-589)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CUB
(11)
Family
:
CUB
(11)
Homo sapiens (Human)
(8)
1a
CUB-2qqkA01
A:149-264
1b
CUB-2qqkA02
A:149-264
Clan
:
GBD
(153)
Family
:
F5_F8_type_C
(45)
Homo sapiens (Human)
(10)
2a
F5_F8_type_C-2qqkA03
A:449-589
2b
F5_F8_type_C-2qqkA04
A:449-589
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