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1W1T
Asym. Unit
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Asym.Unit (186 KB)
Biol.Unit 1 (179 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE B IN COMPLEX WITH THE CYCLIC DIPEPTIDE INHIBITOR CYCLO-(HIS-L-PRO) AT 1.9 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) - 30 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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
[
close entry info
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Hetero Components
(3, 29)
Info
All Hetero Components
1a: CYCLO-(L-HISTIDINE-L-PROLINE) INHI... (CHQa)
1b: CYCLO-(L-HISTIDINE-L-PROLINE) INHI... (CHQb)
1c: CYCLO-(L-HISTIDINE-L-PROLINE) INHI... (CHQc)
1d: CYCLO-(L-HISTIDINE-L-PROLINE) INHI... (CHQd)
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)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CHQ
4
Ligand/Ion
CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR
2
GOL
19
Ligand/Ion
GLYCEROL
3
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:420 , HOH A:2299 , HOH A:2351 , HOH A:2352 , LYS B:386 , HOH B:2347
BINDING SITE FOR RESIDUE SO4 A1511
02
AC2
SOFTWARE
PRO A:281 , SER A:282 , HOH A:2202 , HOH A:2353
BINDING SITE FOR RESIDUE SO4 A1512
03
AC3
SOFTWARE
LYS A:386 , ARG B:420 , HOH B:2354 , HOH B:2414 , HOH B:2415
BINDING SITE FOR RESIDUE SO4 B1508
04
AC4
SOFTWARE
PRO B:281 , SER B:282 , HOH B:2416 , HOH B:2417 , HOH B:2418
BINDING SITE FOR RESIDUE SO4 B1509
05
AC5
SOFTWARE
ASN A:352 , PRO B:454 , ALA B:455 , HOH B:2033
BINDING SITE FOR RESIDUE SO4 B1510
06
AC6
SOFTWARE
THR B:26 , ARG B:343 , ARG B:410 , HOH B:2419 , HOH B:2420 , HOH B:2421 , HOH B:2422
BINDING SITE FOR RESIDUE SO4 B1511
07
AC7
SOFTWARE
TYR A:10 , PHE A:51 , GLY A:96 , TRP A:97 , ASP A:142 , GLU A:144 , MET A:212 , TYR A:214 , ASP A:215 , TRP A:403 , GOL A:1508 , CHQ A:1514 , HOH A:2354 , HOH A:2355
BINDING SITE FOR RESIDUE CHQ A1513
08
AC8
SOFTWARE
TRP A:97 , ASP A:215 , TRP A:220 , GOL A:1508 , GOL A:1509 , CHQ A:1513 , HOH A:2355 , HOH A:2356
BINDING SITE FOR RESIDUE CHQ A1514
09
AC9
SOFTWARE
TYR B:10 , PHE B:51 , GLY B:96 , TRP B:97 , ASP B:142 , GLU B:144 , MET B:212 , TYR B:214 , ASP B:215 , TRP B:403 , GOL B:1507 , CHQ B:1513 , HOH B:2423 , HOH B:2424
BINDING SITE FOR RESIDUE CHQ B1512
10
BC1
SOFTWARE
PHE B:191 , GOL B:1507 , CHQ B:1512 , HOH B:2424
BINDING SITE FOR RESIDUE CHQ B1513
11
BC2
SOFTWARE
PHE A:190 , GLU A:221 , PHE A:239 , GOL A:1509 , GLY B:480
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:2191 , HOH A:2341
BINDING SITE FOR RESIDUE GOL A1501
13
BC4
SOFTWARE
THR A:3 , ARG A:4 , THR A:45 , HIS A:46 , ARG A:89 , TYR A:208 , HOH A:2157 , HOH A:2343
BINDING SITE FOR RESIDUE GOL A1502
14
BC5
SOFTWARE
ARG A:244 , PHE A:259 , PRO A:260 , SER A:261 , HOH A:2174 , TRP B:252
BINDING SITE FOR RESIDUE GOL A1503
15
BC6
SOFTWARE
ARG A:162 , ALA A:204 , LEU A:206 , ASP A:207 , LYS A:284 , HOH A:2344 , HOH A:2345
BINDING SITE FOR RESIDUE GOL A1504
16
BC7
SOFTWARE
PHE A:190 , PHE A:191 , ARG A:194 , HOH A:2346 , TRP B:479 , SER B:484 , ASP B:489 , HOH B:2400
BINDING SITE FOR RESIDUE GOL A1505
17
BC8
SOFTWARE
ARG A:72 , ASN A:76 , GLN A:431 , HOH A:2347
BINDING SITE FOR RESIDUE GOL A1506
18
BC9
SOFTWARE
PHE A:12 , ILE A:13 , PRO A:14 , THR A:15 , SER A:50 , PHE A:51 , ASP A:63 , TYR A:99 , HOH A:2042
BINDING SITE FOR RESIDUE GOL A1507
19
CC1
SOFTWARE
ASP A:215 , ARG A:294 , TRP A:403 , GLN A:407 , CHQ A:1513 , CHQ A:1514 , HOH A:2348 , HOH A:2355
BINDING SITE FOR RESIDUE GOL A1508
20
CC2
SOFTWARE
ASP A:215 , LEU A:216 , TRP A:220 , GLU A:221 , GOL A:1500 , CHQ A:1514 , HOH A:2349
BINDING SITE FOR RESIDUE GOL A1509
21
CC3
SOFTWARE
TYR A:323 , VAL A:326 , GLY A:327 , CYS A:328 , GLU A:329 , VAL A:332 , HOH A:2350
BINDING SITE FOR RESIDUE GOL A1510
22
CC4
SOFTWARE
TRP A:479 , GLY A:480 , TYR A:481 , ASP A:489 , PHE B:190 , PHE B:191 , ARG B:194 , GOL B:1506 , HOH B:2408
BINDING SITE FOR RESIDUE GOL B1500
23
CC5
SOFTWARE
THR B:3 , ARG B:4 , LYS B:5 , ALA B:6 , THR B:45 , GOL B:1504 , HOH B:2409
BINDING SITE FOR RESIDUE GOL B1501
24
CC6
SOFTWARE
TYR B:323 , LEU B:325 , VAL B:326 , GLY B:327 , CYS B:328 , VAL B:332 , HOH B:2279 , HOH B:2282
BINDING SITE FOR RESIDUE GOL B1502
25
CC7
SOFTWARE
PHE B:263 , SER B:264 , ARG B:439 , TYR B:440 , THR B:441 , HOH B:2246 , HOH B:2410
BINDING SITE FOR RESIDUE GOL B1503
26
CC8
SOFTWARE
ARG B:89 , PRO B:178 , GLN B:180 , GOL B:1501 , HOH B:2409 , HOH B:2411
BINDING SITE FOR RESIDUE GOL B1504
27
CC9
SOFTWARE
ARG B:162 , ALA B:204 , LYS B:284 , HOH B:2412 , HOH B:2413
BINDING SITE FOR RESIDUE GOL B1505
28
DC1
SOFTWARE
GLY A:480 , PHE B:190 , GLU B:221 , PHE B:239 , GOL B:1500
BINDING SITE FOR RESIDUE GOL B1506
29
DC2
SOFTWARE
ASP B:215 , TYR B:292 , ARG B:294 , TRP B:403 , GLN B:407 , CHQ B:1512 , CHQ B:1513
BINDING SITE FOR RESIDUE GOL B1507
[
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]
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
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
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_d1w1ta3 (A:447-499)
1b: SCOP_d1w1tb3 (B:447-499)
2a: SCOP_d1w1ta2 (A:292-379)
2b: SCOP_d1w1tb2 (B:292-379)
3a: SCOP_d1w1ta1 (A:3-291,A:380-446)
3b: SCOP_d1w1tb1 (B:3-291,B:380-446)
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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
d1w1ta3
A:447-499
1b
d1w1tb3
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
d1w1ta2
A:292-379
2b
d1w1tb2
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
d1w1ta1
A:3-291,A:380-446
3b
d1w1tb1
B:3-291,B:380-446
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1w1tA01 (A:3-290,A:381-448)
1b: CATH_1w1tB01 (B:3-290,B:381-448)
2a: CATH_1w1tA02 (A:291-380)
2b: CATH_1w1tB02 (B:291-380)
3a: CATH_1w1tA03 (A:449-499)
3b: CATH_1w1tB03 (B:449-499)
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)
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)
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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
1w1tA01
A:3-290,A:381-448
1b
1w1tB01
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
1w1tA02
A:291-380
2b
1w1tB02
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
1w1tA03
A:449-499
3b
1w1tB03
B:449-499
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_18_1w1tB01 (B:5-408)
1b: PFAM_Glyco_hydro_18_1w1tB02 (B:5-408)
2a: PFAM_CBM_5_12_1w1tB03 (B:453-492)
2b: PFAM_CBM_5_12_1w1tB04 (B:453-492)
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Clans
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)
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(
)
Organisms
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)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_18
(72)
Serratia marcescens
(17)
1a
Glyco_hydro_18-1w1tB01
B:5-408
1b
Glyco_hydro_18-1w1tB02
B:5-408
Clan
:
no clan defined [family: CBM_5_12]
(10)
Family
:
CBM_5_12
(10)
Serratia marcescens
(8)
2a
CBM_5_12-1w1tB03
B:453-492
2b
CBM_5_12-1w1tB04
B:453-492
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