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1O6I
Asym. Unit
Info
Asym.Unit (201 KB)
Biol.Unit 1 (194 KB)
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(1)
Title
:
CHITINASE B FROM SERRATIA MARCESCENS COMPLEXED WITH THE CATALYTIC INTERMEDIATE MIMIC CYCLIC DIPEPTIDE CI4.
Authors
:
D. R. Houston, I. Eggleston, B. Synstad, V. G. H. Eijsink, D. M. F. Van Aa
Date
:
03 Oct 02 (Deposition) - 30 Mar 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase-Hydrolase Inhibitor Complex, Chitinase, Catalytic Intermediate Mimic, Cyclic Dipeptide, Hydrolase- Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. R. Houston, I. Eggleston, B. Synstad, V. G. H. Eijsink, D. M. F. Van Aalten
The Cyclic Dipeptide Ci-4 [Cyclo-(L-Arg-D-Pro)] Inhibits Family 18 Chitinases By Structural Mimicry Of A Reaction Intermediate.
Biochem. J. V. 368 23 2002
[
close entry info
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Hetero Components
(3, 39)
Info
All Hetero Components
1a: AMINO({3-[(3S,8AS)-1,4-DIOXOOCTAHY... (0HZa)
1b: AMINO({3-[(3S,8AS)-1,4-DIOXOOCTAHY... (0HZb)
2a: GLYCEROL (GOLa)
2aa: GLYCEROL (GOLaa)
2ab: GLYCEROL (GOLab)
2ac: GLYCEROL (GOLac)
2ad: GLYCEROL (GOLad)
2ae: GLYCEROL (GOLae)
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)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
2z: GLYCEROL (GOLz)
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
0HZ
2
Ligand/Ion
AMINO({3-[(3S,8AS)-1,4-DIOXOOCTAHYDROPYRROLO[1,2-A]PYRAZIN-3-YL]PROPYL}AMINO)METHANIMINIUM
2
GOL
31
Ligand/Ion
GLYCEROL
3
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(39, 39)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:10 , PHE A:12 , GLY A:96 , TRP A:97 , ASP A:142 , GLU A:144 , MET A:212 , TYR A:214 , TRP A:403 , GOL A:1511 , HOH A:2676 , HOH A:2677
BINDING SITE FOR RESIDUE 0HZ A 1516
02
AC2
SOFTWARE
TYR B:10 , PHE B:12 , GLY B:96 , TRP B:97 , ASP B:142 , GLU B:144 , MET B:212 , TYR B:214 , TRP B:403 , GOL B:1512 , GOL B:1515 , HOH B:2723 , HOH B:2737 , HOH B:2738 , HOH B:2739
BINDING SITE FOR RESIDUE 0HZ B 1519
03
AC3
SOFTWARE
TRP A:220 , GOL A:1512 , HOH A:2640 , TYR B:481 , GOL B:1500
BINDING SITE FOR RESIDUE GOL A 1498
04
AC4
SOFTWARE
TRP A:479 , TYR A:481 , ASP A:489 , ALA A:491 , HOH A:2631 , PHE B:190 , PHE B:191 , ARG B:194
BINDING SITE FOR RESIDUE GOL A 1499
05
AC5
SOFTWARE
PRO A:260 , PHE A:263 , SER A:264 , ARG A:439 , TYR A:440 , THR A:441 , HOH A:2401 , HOH A:2641
BINDING SITE FOR RESIDUE GOL A 1500
06
AC6
SOFTWARE
THR A:3 , ARG A:4 , HIS A:46 , ARG A:89 , TYR A:208 , HOH A:2351 , HOH A:2643
BINDING SITE FOR RESIDUE GOL A 1501
07
AC7
SOFTWARE
ARG A:244 , PHE A:259 , PRO A:260 , SER A:261 , HOH A:2644 , TRP B:252
BINDING SITE FOR RESIDUE GOL A 1502
08
AC8
SOFTWARE
ARG A:162 , ALA A:204 , LEU A:206 , ASP A:207 , LYS A:284 , HOH A:2347 , HOH A:2645
BINDING SITE FOR RESIDUE GOL A 1503
09
AC9
SOFTWARE
SER A:300 , SER A:308 , SER A:309 , PRO A:317 , TYR A:318 , PRO A:319 , HOH A:2432 , HOH A:2647
BINDING SITE FOR RESIDUE GOL A 1504
10
BC1
SOFTWARE
LYS A:132 , GLN A:168 , THR A:171 , HOH A:2261 , HOH A:2318 , HOH A:2649 , LYS B:115
BINDING SITE FOR RESIDUE GOL A 1505
11
BC2
SOFTWARE
PHE A:190 , PHE A:191 , SER A:193 , ARG A:194 , HOH A:2652 , HOH A:2653 , TRP B:479 , SER B:484 , ASP B:489 , HOH B:2696
BINDING SITE FOR RESIDUE GOL A 1506
12
BC3
SOFTWARE
ARG A:72 , ASN A:76 , GLN A:431 , HOH A:2654 , HOH A:2655
BINDING SITE FOR RESIDUE GOL A 1507
13
BC4
SOFTWARE
SER A:197 , LEU A:248 , TRP A:250 , HOH A:2384 , HOH A:2658
BINDING SITE FOR RESIDUE GOL A 1508
14
BC5
SOFTWARE
PHE A:231 , GLN A:394 , MET A:434 , ARG A:439 , HOH A:2659
BINDING SITE FOR RESIDUE GOL A 1509
15
BC6
SOFTWARE
ALA A:246 , ASN A:247 , LEU A:248 , GLY A:249 , HOH A:2380 , HOH A:2381 , HOH A:2387 , HOH A:2660 , GLY B:249 , TRP B:250 , SER B:251 , HOH B:2436
BINDING SITE FOR RESIDUE GOL A 1510
16
BC7
SOFTWARE
ARG A:294 , TRP A:403 , GLN A:407 , 0HZ A:1516 , HOH A:2676
BINDING SITE FOR RESIDUE GOL A 1511
17
BC8
SOFTWARE
PHE A:190 , ASP A:215 , LEU A:216 , TRP A:220 , GLU A:221 , LEU A:265 , GOL A:1498 , HOH A:2663 , GOL B:1500
BINDING SITE FOR RESIDUE GOL A 1512
18
BC9
SOFTWARE
THR A:163 , ASN A:166 , TYR A:470 , GLN A:471 , HOH A:2596 , HOH A:2664 , HOH A:2665
BINDING SITE FOR RESIDUE SO4 A 1513
19
CC1
SOFTWARE
ARG A:420 , HOH A:2553 , HOH A:2667 , LYS B:386 , HOH B:2599
BINDING SITE FOR RESIDUE SO4 A 1514
20
CC2
SOFTWARE
PRO A:281 , SER A:282 , HOH A:2669 , HOH A:2670 , HOH A:2672 , HOH A:2673 , HOH A:2674
BINDING SITE FOR RESIDUE SO4 A 1515
21
CC3
SOFTWARE
GLU A:221 , PHE A:239 , GOL A:1498 , GOL A:1512 , HOH A:2652 , TRP B:479 , GLY B:480 , HOH B:2704 , HOH B:2705
BINDING SITE FOR RESIDUE GOL B 1500
22
CC4
SOFTWARE
ARG B:4 , HIS B:46 , ARG B:89 , GOL B:1504 , HOH B:2213 , HOH B:2706
BINDING SITE FOR RESIDUE GOL B 1501
23
CC5
SOFTWARE
TYR B:323 , LEU B:325 , VAL B:326 , GLY B:327 , CYS B:328 , VAL B:332 , HOH B:2494 , HOH B:2498 , HOH B:2499 , HOH B:2708 , HOH B:2709
BINDING SITE FOR RESIDUE GOL B 1502
24
CC6
SOFTWARE
PRO B:260 , PHE B:263 , SER B:264 , ARG B:439 , TYR B:440 , THR B:441 , HOH B:2710
BINDING SITE FOR RESIDUE GOL B 1503
25
CC7
SOFTWARE
ARG B:89 , LEU B:177 , PRO B:178 , GOL B:1501 , HOH B:2711 , HOH B:2712
BINDING SITE FOR RESIDUE GOL B 1504
26
CC8
SOFTWARE
HOH A:2473 , THR B:26 , ARG B:343 , ARG B:410
BINDING SITE FOR RESIDUE GOL B 1505
27
CC9
SOFTWARE
ARG B:162 , ALA B:204 , ASP B:207 , LYS B:284 , HOH B:2346 , HOH B:2714
BINDING SITE FOR RESIDUE GOL B 1506
28
DC1
SOFTWARE
ARG B:4 , LYS B:42 , GLN B:43 , ASP B:419 , HOH B:2715
BINDING SITE FOR RESIDUE GOL B 1507
29
DC2
SOFTWARE
TRP A:479 , GLY A:480 , TYR A:481 , HOH A:2716 , PHE B:190 , GLU B:221 , GOL B:1510 , GOL B:1513
BINDING SITE FOR RESIDUE GOL A 500
30
DC3
SOFTWARE
ASN B:16 , ASN B:19 , HOH B:2033 , HOH B:2052 , HOH B:2717
BINDING SITE FOR RESIDUE GOL B 1509
31
DC4
SOFTWARE
GOL A:500 , GLY B:187 , GLY B:188 , PHE B:190 , PHE B:191 , GOL B:1513 , HOH B:2718 , HOH B:2724
BINDING SITE FOR RESIDUE GOL B 1510
32
DC5
SOFTWARE
ASP A:426 , GLU B:383 , LYS B:386 , HOH B:2720 , HOH B:2721
BINDING SITE FOR RESIDUE GOL B 1511
33
DC6
SOFTWARE
GOL B:1513 , 0HZ B:1519 , HOH B:2723 , HOH B:2724
BINDING SITE FOR RESIDUE GOL B 1512
34
DC7
SOFTWARE
TYR A:481 , GOL A:500 , TRP B:220 , GOL B:1510 , GOL B:1512 , HOH B:2725
BINDING SITE FOR RESIDUE GOL B 1513
35
DC8
SOFTWARE
LYS B:390 , LYS B:393 , ASP B:429 , SER B:430 , HOH B:2618 , HOH B:2620
BINDING SITE FOR RESIDUE GOL B 1514
36
DC9
SOFTWARE
TRP B:403 , GLN B:407 , 0HZ B:1519 , HOH B:2726 , HOH B:2739
BINDING SITE FOR RESIDUE GOL B 1515
37
EC1
SOFTWARE
GLU A:383 , LYS A:386 , ARG B:420 , HOH B:2727 , HOH B:2728 , HOH B:2729 , HOH B:2730
BINDING SITE FOR RESIDUE SO4 B 1516
38
EC2
SOFTWARE
PRO B:281 , SER B:282 , HOH B:2731 , HOH B:2733
BINDING SITE FOR RESIDUE SO4 B 1517
39
EC3
SOFTWARE
ASN A:352 , PRO B:454 , ALA B:455 , HOH B:2653 , HOH B:2655 , HOH B:2736
BINDING SITE FOR RESIDUE SO4 B 1518
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: CHITINASE_18 (A:136-144,B:136-144)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CHITINASE_18
PS01095
Chitinases family 18 active site.
CHIB_SERMA
136-144
2
A:136-144
B:136-144
[
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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_d1o6ia1 (A:447-499)
1b: SCOP_d1o6ib1 (B:447-499)
2a: SCOP_d1o6ia3 (A:292-379)
2b: SCOP_d1o6ib3 (B:292-379)
3a: SCOP_d1o6ia2 (A:3-291,A:380-446)
3b: SCOP_d1o6ib2 (B:3-291,B:380-446)
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)
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)
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)
(
)
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
d1o6ia1
A:447-499
1b
d1o6ib1
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
d1o6ia3
A:292-379
2b
d1o6ib3
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
d1o6ia2
A:3-291,A:380-446
3b
d1o6ib2
B:3-291,B:380-446
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1o6iA01 (A:3-290,A:381-448)
1b: CATH_1o6iB01 (B:3-290,B:381-448)
2a: CATH_1o6iA02 (A:291-380)
2b: CATH_1o6iB02 (B:291-380)
3a: CATH_1o6iA03 (A:449-499)
3b: CATH_1o6iB03 (B:449-499)
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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
1o6iA01
A:3-290,A:381-448
1b
1o6iB01
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
1o6iA02
A:291-380
2b
1o6iB02
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
1o6iA03
A:449-499
3b
1o6iB03
B:449-499
[
close CATH info
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_18_1o6iB01 (B:5-408)
1b: PFAM_Glyco_hydro_18_1o6iB02 (B:5-408)
2a: PFAM_CBM_5_12_1o6iB03 (B:453-492)
2b: PFAM_CBM_5_12_1o6iB04 (B:453-492)
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Clans
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)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_18
(72)
Serratia marcescens
(17)
1a
Glyco_hydro_18-1o6iB01
B:5-408
1b
Glyco_hydro_18-1o6iB02
B:5-408
Clan
:
no clan defined [family: CBM_5_12]
(10)
Family
:
CBM_5_12
(10)
Serratia marcescens
(8)
2a
CBM_5_12-1o6iB03
B:453-492
2b
CBM_5_12-1o6iB04
B:453-492
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