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2XB6
Asym. Unit
Info
Asym.Unit (247 KB)
Biol.Unit 1 (119 KB)
Biol.Unit 2 (122 KB)
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(1)
Title
:
REVISITED CRYSTAL STRUCTURE OF NEUREXIN1BETA-NEUROLIGIN4 COMPLEX
Authors
:
P. Leone, D. Comoletti, G. Ferracci, S. Conrod, S. U. Garcia, P. Taylor, P. Marchot
Date
:
07 Apr 10 (Deposition) - 23 Jun 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Alpha-Beta-Hydrolase Fold, Autism, Conformational Rearrangement, Cell Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Leone, D. Comoletti, G. Ferracci, S. Conrod, S. U. Garcia, P. Taylor Y. Bourne, P. Marchot
Structural Insights Into The Exquisite Selectivity Of Neurexin-Neuroligin Synaptic Interactions
Embo J. V. 29 2461 2010
[
close entry info
]
Hetero Components
(5, 42)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CL
5
Ligand/Ion
CHLORIDE ION
3
EDO
30
Ligand/Ion
1,2-ETHANEDIOL
4
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(42, 42)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:56 , ASN A:102 , HOH A:2124 , ASN D:165
BINDING SITE FOR RESIDUE NAG A 700
02
AC2
SOFTWARE
ASN A:511
BINDING SITE FOR RESIDUE NAG A 701
03
AC3
SOFTWARE
ARG A:232 , GLU A:235 , GLU A:270 , LEU A:272
BINDING SITE FOR RESIDUE EDO A1599
04
AC4
SOFTWARE
GLN A:292 , PRO A:293 , ALA A:294 , LYS A:295
BINDING SITE FOR RESIDUE EDO A1600
05
AC5
SOFTWARE
PHE A:106 , ALA A:107 , ALA A:108 , VAL A:109 , CYS A:146 , ASN A:183 , ASN A:202
BINDING SITE FOR RESIDUE EDO A1601
06
AC6
SOFTWARE
ASN A:386 , EDO A:1608 , GLN C:121 , GLU C:123
BINDING SITE FOR RESIDUE EDO A1602
07
AC7
SOFTWARE
THR A:391 , PRO A:392 , PRO A:433 , ARG A:436
BINDING SITE FOR RESIDUE EDO A1603
08
AC8
SOFTWARE
TYR A:569 , ASP A:580 , HIS A:581 , TYR A:582 , ARG A:583 , HOH A:2125 , HOH A:2126
BINDING SITE FOR RESIDUE EDO A1604
09
AC9
SOFTWARE
ILE A:126 , CYS A:476 , MET A:480 , LYS A:481 , ASP A:491 , PHE A:508
BINDING SITE FOR RESIDUE EDO A1605
10
BC1
SOFTWARE
THR A:137 , TYR A:138 , GLN A:140 , ASP A:141
BINDING SITE FOR RESIDUE EDO A1606
11
BC2
SOFTWARE
GLN A:373
BINDING SITE FOR RESIDUE EDO A1607
12
BC3
SOFTWARE
GLY A:382 , VAL A:384 , EDO A:1602 , HOH A:2129 , LYS C:122
BINDING SITE FOR RESIDUE EDO A1608
13
BC4
SOFTWARE
ARG A:583 , THR A:585
BINDING SITE FOR RESIDUE CL A1609
14
BC5
SOFTWARE
MET A:423 , LYS A:586
BINDING SITE FOR RESIDUE CL A1610
15
BC6
SOFTWARE
ILE B:100 , ASN B:102 , EDO B:1609 , HOH B:2157 , HOH B:2158
BINDING SITE FOR RESIDUE NAG B 700
16
BC7
SOFTWARE
ASN B:511
BINDING SITE FOR RESIDUE NAG B 701
17
BC8
SOFTWARE
GLN B:292 , ALA B:294 , LYS B:295
BINDING SITE FOR RESIDUE EDO B1599
18
BC9
SOFTWARE
VAL B:454 , TYR B:562 , GLN B:567 , TYR B:569 , HIS B:581 , TYR B:582 , HOH B:2159
BINDING SITE FOR RESIDUE EDO B1600
19
CC1
SOFTWARE
MET B:178 , GLN B:329 , THR B:330 , ILE B:331
BINDING SITE FOR RESIDUE EDO B1601
20
CC2
SOFTWARE
HIS B:447 , LEU B:591
BINDING SITE FOR RESIDUE EDO B1602
21
CC3
SOFTWARE
ASP B:-8 , LYS B:54
BINDING SITE FOR RESIDUE EDO B1603
22
CC4
SOFTWARE
GLU B:235 , PRO B:245 , GLY B:271
BINDING SITE FOR RESIDUE EDO B1604
23
CC5
SOFTWARE
PHE B:88 , GLN B:89 , PRO B:90 , GLN B:216 , ALA B:217 , LYS B:219 , TYR B:222 , HOH B:2161
BINDING SITE FOR RESIDUE EDO B1605
24
CC6
SOFTWARE
ASP B:122 , TYR B:336 , LYS B:378 , PHE B:379
BINDING SITE FOR RESIDUE EDO B1606
25
CC7
SOFTWARE
ASP B:122 , LEU B:124 , ILE B:126 , GLU B:375 , GLY B:376 , LYS B:378 , PHE B:444
BINDING SITE FOR RESIDUE EDO B1607
26
CC8
SOFTWARE
ASP B:385 , THR B:391
BINDING SITE FOR RESIDUE EDO B1608
27
CC9
SOFTWARE
TYR B:45 , NAG B:700
BINDING SITE FOR RESIDUE EDO B1609
28
DC1
SOFTWARE
GLY B:84 , ASN B:320
BINDING SITE FOR RESIDUE EDO B1610
29
DC2
SOFTWARE
LYS A:575 , LEU B:62 , ASN B:64 , GLU B:65 , LEU B:67
BINDING SITE FOR RESIDUE EDO B1611
30
DC3
SOFTWARE
GLY B:174 , GLY B:175 , GLU B:179 , GLY B:180 , THR B:181 , MET B:184
BINDING SITE FOR RESIDUE EDO B1612
31
DC4
SOFTWARE
ARG B:583 , THR B:585 , LYS B:586
BINDING SITE FOR RESIDUE CL B1613
32
DC5
SOFTWARE
MET B:423 , LYS B:586
BINDING SITE FOR RESIDUE CL B1614
33
DC6
SOFTWARE
GLU B:592
BINDING SITE FOR RESIDUE CL B1615
34
DC7
SOFTWARE
TRP B:97 , THR B:98 , ILE B:100 , ARG B:101 , GLU C:196 , HOH C:2038
BINDING SITE FOR RESIDUE MES C1289
35
DC8
SOFTWARE
SER B:96 , HOH B:2024 , VAL C:194 , GLU C:196
BINDING SITE FOR RESIDUE EDO C1290
36
DC9
SOFTWARE
LYS C:122 , GLN C:145 , ASN C:169
BINDING SITE FOR RESIDUE EDO C1291
37
EC1
SOFTWARE
TYR C:173 , ASP C:190
BINDING SITE FOR RESIDUE EDO C1292
38
EC2
SOFTWARE
ALA C:110 , ASP C:111 , ARG C:112
BINDING SITE FOR RESIDUE EDO C1293
39
EC3
SOFTWARE
GLU B:85 , GLY C:260 , TYR C:262 , EDO C:1295
BINDING SITE FOR RESIDUE EDO C1294
40
EC4
SOFTWARE
ALA C:114 , TYR C:173 , GLY C:260 , EDO C:1294
BINDING SITE FOR RESIDUE EDO C1295
41
EC5
SOFTWARE
HOH A:2060 , ASP C:137 , VAL C:154 , ILE C:236 , ASN C:238 , HOH C:2012
BINDING SITE FOR RESIDUE CA C1296
42
EC6
SOFTWARE
HOH B:2096 , ASP D:137 , VAL D:154 , ILE D:236 , ASN D:238 , HOH D:2006
BINDING SITE FOR RESIDUE CA D1289
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036576 (G214S, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_036576
G
214
S
NLGNX_HUMAN
Unclassified
---
A/B
G
214
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: LAM_G_DOMAIN (C:87-285,D:87-285)
2: CARBOXYLESTERASE_B_2 (A:144-154,B:144-154)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LAM_G_DOMAIN
PS50025
Laminin G domain profile.
NRX1B_RAT
87-285
2
C:87-285
D:87-285
2
CARBOXYLESTERASE_B_2
PS00941
Carboxylesterases type-B signature 2.
NLGNX_HUMAN
144-154
2
A:144-154
B:144-154
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.6c (A:-1-156 (gaps) | B:-10-156 (gaps))
Exon 1.8 (A:164-209 | B:165-209)
Exon 1.9 (A:209-271 | B:209-271)
Exon 1.10a (A:271-534 | B:271-534)
Exon 1.11d (A:534-598 (gaps) | B:534-598 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.6c
2: Boundary 1.6c/1.8
3: Boundary 1.8/1.9
4: Boundary 1.9/1.10a
5: Boundary 1.10a/1.11d
6: Boundary 1.11d/-
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
ENST00000381095
1a
ENSE00001487516
X:6146904-6146582
323
NLGNX_HUMAN
-
0
0
-
-
1.6c
ENST00000381095
6c
ENSE00001487515
X:6069812-6069036
777
NLGNX_HUMAN
1-158
158
2
A:-1-156 (gaps)
B:-10-156 (gaps)
114
137
1.8
ENST00000381095
8
ENSE00001803933
X:5947473-5947321
153
NLGNX_HUMAN
158-209
52
2
A:164-209
B:165-209
46
45
1.9
ENST00000381095
9
ENSE00001655655
X:5827280-5827095
186
NLGNX_HUMAN
209-271
63
2
A:209-271
B:209-271
63
63
1.10a
ENST00000381095
10a
ENSE00001648911
X:5821907-5821118
790
NLGNX_HUMAN
271-534
264
2
A:271-534
B:271-534
264
264
1.11d
ENST00000381095
11d
ENSE00001827176
X:5811707-5808067
3641
NLGNX_HUMAN
534-816
283
2
A:534-598 (gaps)
B:534-598 (gaps)
65
65
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2xb6c_ (C:)
1b: SCOP_d2xb6d_ (D:)
2a: SCOP_d2xb6a_ (A:)
2b: SCOP_d2xb6b_ (B:)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Laminin G-like module
(37)
Protein domain
:
automated matches
(7)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(3)
1a
d2xb6c_
C:
1b
d2xb6d_
D:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
automated matches
(184)
Protein domain
:
automated matches
(184)
Human (Homo sapiens) [TaxId: 9606]
(42)
2a
d2xb6a_
A:
2b
d2xb6b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2xb6C00 (C:82-288)
1b: CATH_2xb6D00 (D:82-288)
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Homologous Superfamilies
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Organisms
(
)
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)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Human (Homo sapiens)
(49)
1a
2xb6C00
C:82-288
1b
2xb6D00
D:82-288
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_COesterase_2xb6B01 (B:44-590)
1b: PFAM_COesterase_2xb6B02 (B:44-590)
2a: PFAM_Laminin_G_2_2xb6D01 (D:117-266)
2b: PFAM_Laminin_G_2_2xb6D02 (D:117-266)
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Clan
:
AB_hydrolase
(347)
Family
:
COesterase
(79)
Homo sapiens (Human)
(38)
1a
COesterase-2xb6B01
B:44-590
1b
COesterase-2xb6B02
B:44-590
Clan
:
Concanavalin
(293)
Family
:
Laminin_G_2
(14)
Rattus norvegicus (Rat)
(4)
2a
Laminin_G_2-2xb6D01
D:117-266
2b
Laminin_G_2-2xb6D02
D:117-266
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