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1W1Y
Asym. Unit
Info
Asym.Unit (191 KB)
Biol.Unit 1 (185 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE B IN COMPLEX WITH THE CYCLIC DIPEPTIDE INHIBITOR CYCLO-(L-TYR-L-PRO) AT 1.85 A RESOLUTION
Authors
:
D. R. Houston, B. Synstad, V. G. H. Eijsink, I. Eggleston, D. M. F. Van Aalten
Date
:
24 Jun 04 (Deposition) - 10 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase, Glycoside Hydrolase, Chitinase, Structure-Based Inhibitor Design, Cyclic Dipeptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. R. Houston, B. Synstad, V. G. H. Eijsink, M. J. Stark, I. Eggleston, D. M. F. Van Aalten
Structure-Based Exploration Of Cyclic Dipeptide Chitinase Inhibitors
J. Med. Chem. V. 47 5713 2004
[
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Hetero Components
(3, 21)
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)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
3a: CYCLO-(L-TYROSINE-L-PROLINE) INHIB... (TYPa)
3b: CYCLO-(L-TYROSINE-L-PROLINE) INHIB... (TYPb)
3c: CYCLO-(L-TYROSINE-L-PROLINE) INHIB... (TYPc)
3d: CYCLO-(L-TYROSINE-L-PROLINE) INHIB... (TYPd)
3e: CYCLO-(L-TYROSINE-L-PROLINE) INHIB... (TYPe)
3f: CYCLO-(L-TYROSINE-L-PROLINE) INHIB... (TYPf)
3g: CYCLO-(L-TYROSINE-L-PROLINE) INHIB... (TYPg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
12
Ligand/Ion
GLYCEROL
2
SO4
2
Ligand/Ion
SULFATE ION
3
TYP
7
Ligand/Ion
CYCLO-(L-TYROSINE-L-PROLINE) INHIBITOR
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:420 , HOH A:2493 , HOH A:2494 , LYS B:386 , ARG B:420
BINDING SITE FOR RESIDUE SO4 A1505
02
AC2
SOFTWARE
PRO A:281 , SER A:282 , HOH A:2495 , HOH A:2496 , HOH A:2497 , HOH A:2498
BINDING SITE FOR RESIDUE SO4 A1506
03
AC3
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 , ILE A:339 , TRP A:403 , TYP A:1508 , HOH A:2197 , HOH A:2499
BINDING SITE FOR RESIDUE TYP A1507
04
AC4
SOFTWARE
PHE A:12 , PHE A:51 , GLY A:96 , TRP A:97 , TYR A:98 , ASP A:336 , TRP A:403 , TYP A:1507 , HOH A:2134
BINDING SITE FOR RESIDUE TYP A1508
05
AC5
SOFTWARE
TRP A:97 , PHE A:191 , TRP A:220 , HOH A:2500 , HOH A:2501 , TYR B:481 , THR B:483
BINDING SITE FOR RESIDUE TYP A1509
06
AC6
SOFTWARE
TYR B:10 , PHE B:51 , GLY B:96 , TRP B:97 , TYR B:98 , ASP B:142 , GLU B:144 , TYR B:214 , ASP B:215 , TYR B:292 , ARG B:294 , TRP B:403 , TYP B:1507 , TYP B:1508 , HOH B:2213 , HOH B:2349
BINDING SITE FOR RESIDUE TYP B1506
07
AC7
SOFTWARE
PHE B:12 , PHE B:51 , GLY B:96 , TRP B:97 , TYR B:98 , ASP B:334 , ASP B:336 , TRP B:403 , TYP B:1506 , HOH B:2368 , HOH B:2562 , HOH B:2563
BINDING SITE FOR RESIDUE TYP B1507
08
AC8
SOFTWARE
TYR A:481 , THR A:483 , HOH A:2455 , TRP B:97 , TRP B:220 , TYP B:1506 , HOH B:2363 , HOH B:2364 , HOH B:2564
BINDING SITE FOR RESIDUE TYP B1508
09
AC9
SOFTWARE
ARG B:162 , ASN B:166 , PRO B:178 , ALA B:204 , PRO B:205 , LEU B:206 , ASP B:207 , LYS B:284 , VAL B:326 , TYR B:353 , GLN B:372 , ASN B:373 , HOH B:2566
BINDING SITE FOR RESIDUE TYP B1509
10
BC1
SOFTWARE
ASP A:215 , LEU A:216 , ALA A:217 , TRP A:220 , GLU A:221 , LEU A:265 , HOH A:2484
BINDING SITE FOR RESIDUE GOL A1499
11
BC2
SOFTWARE
TRP A:479 , ILE A:482 , THR A:483 , ASP A:489 , HOH A:2485 , PHE B:190 , PHE B:191 , ARG B:194
BINDING SITE FOR RESIDUE GOL A1500
12
BC3
SOFTWARE
PRO A:260 , PHE A:263 , SER A:264 , ARG A:439 , TYR A:440 , THR A:441 , HOH A:2307 , HOH A:2486
BINDING SITE FOR RESIDUE GOL A1501
13
BC4
SOFTWARE
ARG A:244 , PHE A:259 , PRO A:260 , SER A:261 , HOH A:2487 , TRP B:252
BINDING SITE FOR RESIDUE GOL A1502
14
BC5
SOFTWARE
ARG A:162 , ALA A:204 , ASP A:207 , LYS A:284 , HOH A:2258 , HOH A:2488 , HOH A:2489
BINDING SITE FOR RESIDUE GOL A1503
15
BC6
SOFTWARE
PHE A:190 , GLU A:221 , HOH A:2491 , HOH A:2492 , TRP B:479 , GLY B:480 , HOH B:2558
BINDING SITE FOR RESIDUE GOL A1504
16
BC7
SOFTWARE
ARG B:4 , HIS B:46 , ARG B:89 , HOH B:2148 , HOH B:2151 , HOH B:2553 , HOH B:2554
BINDING SITE FOR RESIDUE GOL B1500
17
BC8
SOFTWARE
PRO B:260 , PHE B:263 , SER B:264 , ARG B:439 , TYR B:440 , THR B:441 , HOH B:2555 , HOH B:2556 , HOH B:2557
BINDING SITE FOR RESIDUE GOL B1501
18
BC9
SOFTWARE
PHE A:190 , ARG A:194 , TRP B:479 , ILE B:482 , THR B:483 , ASP B:489 , HOH B:2540 , HOH B:2546 , HOH B:2558
BINDING SITE FOR RESIDUE GOL B1502
19
CC1
SOFTWARE
GLY A:480 , HOH A:2485 , PHE B:190 , GLU B:221 , GOL B:1504 , HOH B:2559 , HOH B:2560 , HOH B:2561
BINDING SITE FOR RESIDUE GOL B1503
20
CC2
SOFTWARE
ASP B:215 , LEU B:216 , ALA B:217 , TRP B:220 , GLU B:221 , LEU B:265 , GOL B:1503 , HOH B:2561
BINDING SITE FOR RESIDUE GOL B1504
21
CC3
SOFTWARE
TRP A:252 , ARG B:244 , PHE B:259 , PRO B:260 , SER B:261
BINDING SITE FOR RESIDUE GOL B1505
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
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_d1w1ya3 (A:447-499)
1b: SCOP_d1w1yb3 (B:447-499)
2a: SCOP_d1w1ya2 (A:292-379)
2b: SCOP_d1w1yb2 (B:292-379)
3a: SCOP_d1w1ya1 (A:3-291,A:380-446)
3b: SCOP_d1w1yb1 (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
d1w1ya3
A:447-499
1b
d1w1yb3
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
d1w1ya2
A:292-379
2b
d1w1yb2
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
d1w1ya1
A:3-291,A:380-446
3b
d1w1yb1
B:3-291,B:380-446
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1w1yA01 (A:3-290,A:381-448)
1b: CATH_1w1yB01 (B:3-290,B:381-448)
2a: CATH_1w1yA02 (A:291-380)
2b: CATH_1w1yB02 (B:291-380)
3a: CATH_1w1yA03 (A:449-499)
3b: CATH_1w1yB03 (B:449-499)
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Topologies
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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)
Serratia marcescens. Organism_taxid: 615.
(19)
1a
1w1yA01
A:3-290,A:381-448
1b
1w1yB01
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.
(17)
2a
1w1yA02
A:291-380
2b
1w1yB02
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.
(13)
3a
1w1yA03
A:449-499
3b
1w1yB03
B:449-499
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_18_1w1yB01 (B:5-408)
1b: PFAM_Glyco_hydro_18_1w1yB02 (B:5-408)
2a: PFAM_CBM_5_12_1w1yB03 (B:453-492)
2b: PFAM_CBM_5_12_1w1yB04 (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_18-1w1yB01
B:5-408
1b
Glyco_hydro_18-1w1yB02
B:5-408
Clan
:
no clan defined [family: CBM_5_12]
(10)
Family
:
CBM_5_12
(10)
Serratia marcescens
(8)
2a
CBM_5_12-1w1yB03
B:453-492
2b
CBM_5_12-1w1yB04
B:453-492
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