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1HJW
Asym. Unit
Info
Asym.Unit (138 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (67 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HCGP-39 IN COMPLEX WITH CHITIN OCTAMER
Authors
:
D. R. Houston, A. D. Recklies, J. C. Krupa, D. M. F. Van Aalten
Date
:
28 Feb 03 (Deposition) - 11 Mar 03 (Release) - 27 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Sugar Binding Protein, Lectin, Chi-Lectin, Chitinase, Chondrocyte
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. R. Houston, A. D. Recklies, J. C. Krupa, D. M. F. Van Aalten
Structure And Ligand-Induced Conformational Change Of The 39-Kda Glycoprotein From Human Articular Chondrocytes
J. Biol. Chem. V. 278 30206 2003
[
close entry info
]
Hetero Components
(3, 25)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
2m: N-ACETYL-D-GLUCOSAMINE (NAGm)
2n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
7
Ligand/Ion
GLYCEROL
2
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:233 , HOH A:2098 , ARG B:224 , GLU B:227 , ARG B:233
BINDING SITE FOR RESIDUE SO4 A1392
02
AC2
SOFTWARE
LYS A:182 , ARG A:233 , TYR A:239 , ARG A:246 , GLU B:227
BINDING SITE FOR RESIDUE SO4 A1394
03
AC3
SOFTWARE
ARG A:117 , LYS A:121
BINDING SITE FOR RESIDUE SO4 A1396
04
AC4
SOFTWARE
GLU A:227 , ARG B:233 , TYR B:239 , ARG B:246 , HOH B:2159
BINDING SITE FOR RESIDUE SO4 B1386
05
AC5
SOFTWARE
ALA A:211 , SER A:279 , GLY A:280 , HOH A:2174 , ARG B:144
BINDING SITE FOR RESIDUE GOL A1386
06
AC6
SOFTWARE
NAG A:2 , TRP A:212
BINDING SITE FOR RESIDUE GOL A1387
07
AC7
SOFTWARE
PHE A:42 , ASP A:44
BINDING SITE FOR RESIDUE GOL A1388
08
AC8
SOFTWARE
TYR A:34 , TRP A:71 , HOH A:2175 , HOH A:2176
BINDING SITE FOR RESIDUE GOL A1389
09
AC9
SOFTWARE
GLN A:315 , HOH A:2177 , HOH A:2178 , GLN B:315 , HOH B:2136
BINDING SITE FOR RESIDUE GOL A1399
10
BC1
SOFTWARE
ARG B:117
BINDING SITE FOR RESIDUE GOL B1384
11
BC2
SOFTWARE
NAG B:-3 , TRP B:31 , ARG B:35 , THR B:288
BINDING SITE FOR RESIDUE GOL B1385
12
BC3
SOFTWARE
ASN A:60 , ILE A:61 , SER A:62 , HOH A:2028 , HOH A:2171
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1384 THROUGH NDG A1385 BOUND TO ASN A 60
13
BC4
SOFTWARE
ASN B:60 , SER B:62 , HOH B:2157
BINDING SITE FOR MONO-SACCHARIDE NAG B1383 BOUND TO ASN B 60
14
BC5
SOFTWARE
NAG A:-1 , TRP A:99 , TYR A:141 , GLY A:181 , MET A:204 , ASP A:207 , PHE A:208 , ARG A:263 , GOL A:1387 , HOH A:2006 , HOH A:2007 , HOH A:2008 , HOH A:2084
BINDING SITE FOR DI-SACCHARIDE NAG A 1 AND NAG A 2
15
BC6
SOFTWARE
NAG A:-2 , NAG A:2 , TYR A:27 , TRP A:99 , LEU A:140 , TYR A:141 , MET A:204 , TYR A:206 , ASP A:207 , ARG A:263 , TRP A:352 , HOH A:2006
BINDING SITE FOR DI-SACCHARIDE NAG A -1 AND NAG A 1
16
BC7
SOFTWARE
NAG A:-3 , NAG A:1 , TYR A:27 , TRP A:31 , GLY A:98 , TRP A:99 , ASN A:100 , LEU A:140 , MET A:204 , TYR A:206 , ASP A:207 , ARG A:263 , TRP A:352 , LEU A:356 , HOH A:2001 , HOH A:2002 , HOH A:2003 , HOH A:2004
BINDING SITE FOR DI-SACCHARIDE NAG A -2 AND NAG A -1
17
BC8
SOFTWARE
NAG A:-4 , NAG A:-1 , TRP A:31 , GLY A:98 , TRP A:99 , ASN A:100 , ARG A:263 , TRP A:352 , LEU A:356 , HOH A:2001 , HOH A:2002 , HOH A:2003 , HOH A:2004
BINDING SITE FOR DI-SACCHARIDE NAG A -3 AND NAG A -2
18
BC9
SOFTWARE
NAG A:-2 , TRP A:31 , TYR A:34 , GLU A:70 , ASN A:100 , HOH A:2004 , HOH A:2005
BINDING SITE FOR DI-SACCHARIDE NAG A -4 AND NAG A -3
19
CC1
SOFTWARE
NAG B:-1 , TRP B:99 , TYR B:141 , GLY B:181 , MET B:204 , ASP B:207 , HOH B:2004 , HOH B:2005
BINDING SITE FOR DI-SACCHARIDE NAG B 1 AND NAG B 2
20
CC2
SOFTWARE
NAG B:-2 , NAG B:2 , TYR B:27 , TRP B:99 , LEU B:140 , TYR B:141 , MET B:204 , TYR B:206 , ASP B:207 , ARG B:263 , TRP B:352 , HOH B:2004
BINDING SITE FOR DI-SACCHARIDE NAG B -1 AND NAG B 1
21
CC3
SOFTWARE
NAG B:-3 , NAG B:1 , TYR B:27 , TRP B:31 , TRP B:99 , ASN B:100 , LEU B:140 , MET B:204 , TYR B:206 , ASP B:207 , ARG B:263 , GLU B:290 , TRP B:352 , HOH B:2001 , HOH B:2100
BINDING SITE FOR DI-SACCHARIDE NAG B -2 AND NAG B -1
22
CC4
SOFTWARE
NAG B:-1 , TRP B:31 , TRP B:99 , ASN B:100 , GLU B:290 , TRP B:352 , GOL B:1385 , HOH B:2001 , HOH B:2002 , HOH B:2003 , HOH B:2100
BINDING SITE FOR DI-SACCHARIDE NAG B -3 AND NAG B -2
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_019838 (R145G, chain A/B, )
2: VAR_019839 (I311T, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_019838
R
145
G
CH3L1_HUMAN
Polymorphism
880633
A/B
R
145
G
2
UniProt
VAR_019839
I
311
T
CH3L1_HUMAN
Polymorphism
1049407
A/B
I
311
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(8, 16)
Info
All Exons
Exon 1.3 (A:22-86 | B:22-86)
Exon 1.4 (A:86-105 | B:86-105)
Exon 1.5 (A:105-155 | B:105-155)
Exon 1.6a (A:156-196 | B:156-196)
Exon 1.7b (A:196-237 | B:196-237)
Exon 1.8a (A:238-298 | B:238-298)
Exon 1.8d (A:299-337 | B:299-337)
Exon 1.8i (A:338-383 | B:338-383)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3
2: Boundary 1.3/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6a
5: Boundary 1.6a/1.7b
6: Boundary 1.7b/1.8a
7: Boundary 1.8a/1.8d
8: Boundary 1.8d/1.8i
9: Boundary 1.8i/-
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
1.1b
ENST00000255409
1b
ENSE00001918937
chr1:
203155877-203155727
151
CH3L1_HUMAN
1-9
9
0
-
-
1.2
ENST00000255409
2
ENSE00001639449
chr1:
203155473-203155444
30
CH3L1_HUMAN
9-19
11
0
-
-
1.3
ENST00000255409
3
ENSE00001784822
chr1:
203154513-203154312
202
CH3L1_HUMAN
19-86
68
2
A:22-86
B:22-86
65
65
1.4
ENST00000255409
4
ENSE00001795703
chr1:
203153760-203153704
57
CH3L1_HUMAN
86-105
20
2
A:86-105
B:86-105
20
20
1.5
ENST00000255409
5
ENSE00001644034
chr1:
203152919-203152769
151
CH3L1_HUMAN
105-155
51
2
A:105-155
B:105-155
51
51
1.6a
ENST00000255409
6a
ENSE00001648436
chr1:
203151980-203151859
122
CH3L1_HUMAN
156-196
41
2
A:156-196
B:156-196
41
41
1.7b
ENST00000255409
7b
ENSE00001713191
chr1:
203150413-203150290
124
CH3L1_HUMAN
196-237
42
2
A:196-237
B:196-237
42
42
1.8a
ENST00000255409
8a
ENSE00001045187
chr1:
203149780-203149598
183
CH3L1_HUMAN
238-298
61
2
A:238-298
B:238-298
61
61
1.8d
ENST00000255409
8d
ENSE00001045185
chr1:
203149005-203148889
117
CH3L1_HUMAN
299-337
39
2
A:299-337
B:299-337
39
39
1.8i
ENST00000255409
8i
ENSE00001045180
chr1:
203148713-203148059
655
CH3L1_HUMAN
338-383
46
2
A:338-383
B:338-383
46
46
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1hjwa2 (A:261-328)
1b: SCOP_d1hjwb2 (B:261-328)
2a: SCOP_d1hjwa1 (A:22-260,A:329-383)
2b: SCOP_d1hjwb1 (B:22-260,B:329-383)
View:
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Classes
(
)
(
)
Folds
(
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(
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Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FKBP-like
(309)
Superfamily
:
Chitinase insertion domain
(107)
Family
:
Chitinase insertion domain
(107)
Protein domain
:
Chitinase-3 like protein 1 (GP-39, YKL-40)
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1hjwa2
A:261-328
1b
d1hjwb2
B:261-328
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
Type II chitinase
(131)
Protein domain
:
Chitinase-3 like protein 1 (GP-39, YKL-40)
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d1hjwa1
A:22-260,A:329-383
2b
d1hjwb1
B:22-260,B:329-383
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1hjwA01 (A:22-259,A:330-383)
1b: CATH_1hjwB01 (B:22-259,B:330-383)
2a: CATH_1hjwA02 (A:260-329)
2b: CATH_1hjwB02 (B:260-329)
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Homologous Superfamilies
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Human (Homo sapiens)
(94)
1a
1hjwA01
A:22-259,A:330-383
1b
1hjwB01
B:22-259,B:330-383
Architecture
:
Roll
(3276)
Topology
:
Chitinase A; domain 3
(225)
Homologous Superfamily
:
[code=3.10.50.10, no name defined]
(121)
Human (Homo sapiens)
(19)
2a
1hjwA02
A:260-329
2b
1hjwB02
B:260-329
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Asym.Unit (138 KB)
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