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1UR8
Asym. Unit
Info
Asym.Unit (182 KB)
Biol.Unit 1 (176 KB)
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(1)
Title
:
INTERACTIONS OF A FAMILY 18 CHITINASE WITH THE DESIGNED INHIBITOR HM508, AND ITS DEGRADATION PRODUCT, CHITOBIONO-DELTA-LACTONE
Authors
:
G. Vaaje-Kolstad, A. Vasella, M. G. Peter, C. Netter, D. R. Houston, B. Westereng, B. Synstad, V. G. H. Eijsink, D. M. F. Van Aalten
Date
:
27 Oct 03 (Deposition) - 27 Apr 04 (Release) - 15 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase, Chitinase, Inhibition, Lactone, Chitin Degradation, Glycosidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Vaaje-Kolstad, A. Vasella, M. G. Peter, C. Netter, D. R. Houston, B. Westereng, B. Synstad, V. G. H. Eijsink, D. M. F. Van Aalten
Interactions Of A Family 18 Chitinase With The Designed Inhibitor Hm508 And Its Degradation Product, Chitobiono- Delta-Lactone.
J. Biol. Chem. V. 279 3612 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 20)
Info
All Hetero Components
1a: 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-... (GDLa)
1b: 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-... (GDLb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDL
2
Ligand/Ion
2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
2
GOL
9
Ligand/Ion
GLYCEROL
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:420 , HOH A:2306 , HOH A:2343 , HOH A:2344 , HOH A:2345 , LYS B:386
BINDING SITE FOR RESIDUE SO4 A1503
02
AC2
SOFTWARE
PRO A:14 , ASN A:16 , GLN A:17 , VAL A:28 , ARG A:333
BINDING SITE FOR RESIDUE SO4 A1504
03
AC3
SOFTWARE
PRO A:281 , SER A:282 , HOH A:2347 , HOH A:2348
BINDING SITE FOR RESIDUE SO4 A1505
04
AC4
SOFTWARE
LYS A:386 , ARG B:420 , HOH B:2394 , HOH B:2395 , HOH B:2396
BINDING SITE FOR RESIDUE SO4 B1507
05
AC5
SOFTWARE
PRO B:281 , SER B:282 , HOH B:2264 , HOH B:2397 , HOH B:2398
BINDING SITE FOR RESIDUE SO4 B1508
06
AC6
SOFTWARE
ASN B:16 , GLN B:17 , VAL B:28 , ARG B:333 , HOH B:2035
BINDING SITE FOR RESIDUE SO4 B1509
07
AC7
SOFTWARE
ARG B:294 , HOH B:2284 , HOH B:2400 , NAG B:2501 , GDL B:2502
BINDING SITE FOR RESIDUE SO4 B1510
08
AC8
SOFTWARE
PRO A:260 , PHE A:263 , SER A:264 , ARG A:439 , TYR A:440 , THR A:441 , HOH A:2210 , HOH A:2342
BINDING SITE FOR RESIDUE GOL A1499
09
AC9
SOFTWARE
ASN A:55 , SER A:56 , PRO A:64 , ASN A:109 , THR A:436 , HOH A:2095 , HOH A:2099
BINDING SITE FOR RESIDUE GOL A1500
10
BC1
SOFTWARE
ARG A:343 , GLN A:347 , ARG A:410
BINDING SITE FOR RESIDUE GOL A1501
11
BC2
SOFTWARE
PRO B:260 , PHE B:263 , SER B:264 , HOH B:2254 , HOH B:2386
BINDING SITE FOR RESIDUE GOL B1500
12
BC3
SOFTWARE
TYR B:323 , LEU B:325 , VAL B:326 , GLY B:327 , GLU B:329 , VAL B:332
BINDING SITE FOR RESIDUE GOL B1501
13
BC4
SOFTWARE
PHE A:190 , SER A:193 , ARG A:194 , TRP B:479 , THR B:483 , SER B:484 , ASP B:489 , HOH B:2387
BINDING SITE FOR RESIDUE GOL B1502
14
BC5
SOFTWARE
ARG B:162 , ALA B:204 , PRO B:205 , ASP B:207 , LYS B:284
BINDING SITE FOR RESIDUE GOL B1503
15
BC6
SOFTWARE
TRP A:479 , GLY A:480 , TYR A:481 , ILE A:482 , PHE B:190 , PHE B:191 , ARG B:194 , HOH B:2388 , HOH B:2389
BINDING SITE FOR RESIDUE GOL B1504
16
BC7
SOFTWARE
PRO B:454 , ALA B:455 , HOH B:2390 , HOH B:2391 , HOH B:2392 , HOH B:2393
BINDING SITE FOR RESIDUE GOL B1505
17
BC8
SOFTWARE
TYR A:10 , PHE A:51 , GLY A:96 , TRP A:97 , TYR A:98 , ASP A:142 , GLU A:144 , MET A:212 , TYR A:214 , ASP A:215 , TYR A:292 , ARG A:294 , TRP A:403 , GLN A:407 , HOH A:2084 , HOH A:2123 , HOH A:2177 , HOH A:2350
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A2501 THROUGH GDL A2502
18
BC9
SOFTWARE
TYR B:10 , PHE B:51 , TRP B:97 , TYR B:98 , ASP B:142 , GLU B:144 , MET B:212 , TYR B:214 , ASP B:215 , TYR B:292 , ARG B:294 , TRP B:403 , GLN B:407 , SO4 B:1510 , HOH B:2404 , HOH B:2406
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B2501 THROUGH GDL B2502
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1ur8a1 (A:447-499)
1b: SCOP_d1ur8b1 (B:447-499)
2a: SCOP_d1ur8a3 (A:292-379)
2b: SCOP_d1ur8b3 (B:292-379)
3a: SCOP_d1ur8a2 (A:3-291,A:380-446)
3b: SCOP_d1ur8b2 (B:3-291,B:380-446)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
WW domain-like
(101)
Superfamily
:
Carbohydrate binding domain
(20)
Family
:
Carbohydrate binding domain
(20)
Protein domain
:
Chitinase B, C-terminal domain
(18)
Serratia marcescens [TaxId: 615]
(18)
1a
d1ur8a1
A:447-499
1b
d1ur8b1
B:447-499
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 B
(18)
Serratia marcescens [TaxId: 615]
(18)
2a
d1ur8a3
A:292-379
2b
d1ur8b3
B:292-379
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 B, catalytic domain
(18)
Serratia marcescens [TaxId: 615]
(18)
3a
d1ur8a2
A:3-291,A:380-446
3b
d1ur8b2
B:3-291,B:380-446
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1ur8A01 (A:3-290,A:381-448)
1b: CATH_1ur8B01 (B:3-290,B:381-448)
2a: CATH_1ur8A02 (A:291-380)
2b: CATH_1ur8B02 (B:291-380)
3a: CATH_1ur8A03 (A:449-499)
3b: CATH_1ur8B03 (B:449-499)
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)
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)
Architectures
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Serratia marcescens. Organism_taxid: 615. Strain: bjl200.
(4)
1a
1ur8A01
A:3-290,A:381-448
1b
1ur8B01
B:3-290,B:381-448
Architecture
:
Roll
(3276)
Topology
:
Chitinase A; domain 3
(225)
Homologous Superfamily
:
[code=3.10.50.10, no name defined]
(121)
Serratia marcescens. Organism_taxid: 615. Strain: bjl200.
(4)
2a
1ur8A02
A:291-380
2b
1ur8B02
B:291-380
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Seminal Fluid Protein PDC-109 (Domain B)
(33)
Homologous Superfamily
:
[code=2.10.10.20, no name defined]
(20)
Serratia marcescens. Organism_taxid: 615. Strain: bjl200.
(4)
3a
1ur8A03
A:449-499
3b
1ur8B03
B:449-499
[
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]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_18_1ur8B01 (B:5-408)
1b: PFAM_Glyco_hydro_18_1ur8B02 (B:5-408)
2a: PFAM_CBM_5_12_1ur8B03 (B:453-492)
2b: PFAM_CBM_5_12_1ur8B04 (B:453-492)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_18
(72)
Serratia marcescens
(17)
1a
Glyco_hydro_18-1ur8B01
B:5-408
1b
Glyco_hydro_18-1ur8B02
B:5-408
Clan
:
no clan defined [family: CBM_5_12]
(10)
Family
:
CBM_5_12
(10)
Serratia marcescens
(8)
2a
CBM_5_12-1ur8B03
B:453-492
2b
CBM_5_12-1ur8B04
B:453-492
[
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]
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Asym.Unit (182 KB)
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