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1NHC
Asym. Unit
Info
Asym.Unit (341 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 KB)
Biol.Unit 3 (62 KB)
Biol.Unit 4 (62 KB)
Biol.Unit 5 (63 KB)
Biol.Unit 6 (62 KB)
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(1)
Title
:
STRUCTURAL INSIGHTS INTO THE PROCESSIVITY OF ENDOPOLYGALACTURONASE I FROM ASPERGILLUS NIGER
Authors
:
G. Van Pouderoyen, H. J. Snijder, J. A. Benen, B. W. Dijkstra
Date
:
19 Dec 02 (Deposition) - 25 Nov 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Beta-Helix, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Van Pouderoyen, H. J. Snijder, J. A. Benen, B. W. Dijkstra
Structural Insights Into The Processivity Of Endopolygalacturonase I From Aspergillus Niger.
Febs Lett. V. 554 462 2003
[
close entry info
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Hetero Components
(5, 46)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
3e: ALPHA-D-MANNOSE (MANe)
3f: ALPHA-D-MANNOSE (MANf)
3g: ALPHA-D-MANNOSE (MANg)
3h: ALPHA-D-MANNOSE (MANh)
3i: ALPHA-D-MANNOSE (MANi)
3j: ALPHA-D-MANNOSE (MANj)
3k: ALPHA-D-MANNOSE (MANk)
3l: ALPHA-D-MANNOSE (MANl)
3m: ALPHA-D-MANNOSE (MANm)
3n: ALPHA-D-MANNOSE (MANn)
3o: ALPHA-D-MANNOSE (MANo)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
5l: SULFATE ION (SO4l)
5m: SULFATE ION (SO4m)
5n: SULFATE ION (SO4n)
5o: SULFATE ION (SO4o)
5p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
GOL
5
Ligand/Ion
GLYCEROL
3
MAN
15
Ligand/Ion
ALPHA-D-MANNOSE
4
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SO4
16
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(46, 46)
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)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:44
BINDING SITE FOR RESIDUE MAN A 401
02
AC2
SOFTWARE
PHE A:37 , GLU A:42 , SER A:46
BINDING SITE FOR RESIDUE MAN A 402
03
AC3
SOFTWARE
TYR A:197 , SER A:217 , ASN A:246 , NAG A:404 , HOH A:2843
BINDING SITE FOR RESIDUE NAG A 403
04
AC4
SOFTWARE
NAG A:403 , HOH A:2941
BINDING SITE FOR RESIDUE NAG A 404
05
AC5
SOFTWARE
SER B:44
BINDING SITE FOR RESIDUE MAN B 401
06
AC6
SOFTWARE
PHE B:37 , GLU B:42 , SER B:46 , SER E:33
BINDING SITE FOR RESIDUE MAN B 402
07
AC7
SOFTWARE
SER B:217 , SER B:219 , ASN B:246 , NAG B:404 , HOH B:2871
BINDING SITE FOR RESIDUE NAG B 403
08
AC8
SOFTWARE
NAG B:403 , BMA B:405 , ASN E:299
BINDING SITE FOR RESIDUE NAG B 404
09
AC9
SOFTWARE
NAG B:404 , MAN B:406 , GLU E:298 , ASN E:299 , HOH E:2871
BINDING SITE FOR RESIDUE BMA B 405
10
BC1
SOFTWARE
BMA B:405 , MAN B:407 , MAN D:408
BINDING SITE FOR RESIDUE MAN B 406
11
BC2
SOFTWARE
MAN B:406 , HOH B:2748 , ASN E:299
BINDING SITE FOR RESIDUE MAN B 407
12
BC3
SOFTWARE
MAN B:406 , LYS D:358
BINDING SITE FOR RESIDUE MAN D 408
13
BC4
SOFTWARE
SER C:44
BINDING SITE FOR RESIDUE MAN C 401
14
BC5
SOFTWARE
GLU C:42 , SER C:46
BINDING SITE FOR RESIDUE MAN C 402
15
BC6
SOFTWARE
SER C:217 , ASN C:246 , HOH C:2953 , HOH C:2956
BINDING SITE FOR RESIDUE NAG C 403
16
BC7
SOFTWARE
SER D:44
BINDING SITE FOR RESIDUE MAN D 401
17
BC8
SOFTWARE
SER C:51 , PHE D:37 , GLU D:42 , SER D:46 , HOH D:2840 , HOH D:2854 , HOH D:2904 , HOH D:2922
BINDING SITE FOR RESIDUE MAN D 402
18
BC9
SOFTWARE
SER D:217 , SER D:219 , ASN D:246 , NAG D:404 , HOH D:2769
BINDING SITE FOR RESIDUE NAG D 403
19
CC1
SOFTWARE
NAG D:403 , MAN D:405
BINDING SITE FOR RESIDUE NAG D 404
20
CC2
SOFTWARE
LYS B:354 , GLU C:298 , ASN C:299 , HOH C:2918 , HOH C:2969 , NAG D:404
BINDING SITE FOR RESIDUE MAN D 405
21
CC3
SOFTWARE
SER E:41 , SER E:44 , GOL E:2005
BINDING SITE FOR RESIDUE MAN E 401
22
CC4
SOFTWARE
PHE E:37 , GLU E:42 , SER E:46
BINDING SITE FOR RESIDUE MAN E 402
23
CC5
SOFTWARE
TYR E:197 , SER E:217 , ASN E:246 , HOH E:2857 , HOH E:2883
BINDING SITE FOR RESIDUE NAG E 403
24
CC6
SOFTWARE
PHE F:37 , GLU F:42 , SER F:46
BINDING SITE FOR RESIDUE MAN F 402
25
CC7
SOFTWARE
TYR F:197 , SER F:217 , SER F:219 , ASN F:246 , HOH F:2915
BINDING SITE FOR RESIDUE NAG F 403
26
CC8
SOFTWARE
ALA A:40 , SER A:41 , PRO A:61 , HOH A:2781
BINDING SITE FOR RESIDUE SO4 A 2701
27
CC9
SOFTWARE
ALA B:40 , SER B:41 , PRO B:61
BINDING SITE FOR RESIDUE SO4 B 2702
28
DC1
SOFTWARE
ALA C:40 , SER C:41 , PRO C:61 , HOH C:2789 , HOH C:2943 , HOH C:2951
BINDING SITE FOR RESIDUE SO4 C 2703
29
DC2
SOFTWARE
SER D:39 , ALA D:40 , SER D:41 , PRO D:61 , HOH D:2767 , HOH D:2909
BINDING SITE FOR RESIDUE SO4 D 2704
30
DC3
SOFTWARE
ALA E:40 , SER E:41 , PRO E:61 , HOH E:2746 , HOH E:2928 , HOH E:2942 , HOH E:2957
BINDING SITE FOR RESIDUE SO4 E 2705
31
DC4
SOFTWARE
ALA F:40 , SER F:41 , PRO F:61 , HOH F:2766
BINDING SITE FOR RESIDUE SO4 F 2706
32
DC5
SOFTWARE
PHE A:85 , GLY A:86 , TYR A:87 , ARG A:118 , PHE C:85 , GLY C:86 , TYR C:87 , ARG C:118 , HOH C:2736 , HOH C:2739 , HOH C:2753 , HOH C:2755 , HOH C:2770 , HOH C:2785
BINDING SITE FOR RESIDUE SO4 C 2707
33
DC6
SOFTWARE
PHE E:85 , GLY E:86 , TYR E:87 , ARG E:118 , HOH E:2749 , HOH E:2752 , HOH E:2759 , HOH E:2773 , HOH E:2774 , HOH E:2804 , PHE F:85 , GLY F:86 , TYR F:87 , ARG F:118
BINDING SITE FOR RESIDUE SO4 E 2708
34
DC7
SOFTWARE
ASP A:207 , HIS A:229 , ARG A:262 , LYS A:264 , HOH A:2881 , HOH A:2882 , HOH A:2904
BINDING SITE FOR RESIDUE SO4 A 2711
35
DC8
SOFTWARE
ASP B:207 , HIS B:229 , ARG B:262 , HOH B:2821 , HOH B:2823 , HOH B:2855
BINDING SITE FOR RESIDUE SO4 B 2712
36
DC9
SOFTWARE
ASP C:207 , HIS C:229 , ARG C:262 , LYS C:264 , HOH C:2851 , HOH C:2853 , HOH C:2942
BINDING SITE FOR RESIDUE SO4 C 2713
37
EC1
SOFTWARE
ASP D:207 , HIS D:229 , ARG D:262 , HOH D:2765 , HOH D:2780 , HOH D:2785
BINDING SITE FOR RESIDUE SO4 D 2714
38
EC2
SOFTWARE
ASP E:207 , HIS E:229 , ARG E:262 , LYS E:264 , HOH E:2783 , HOH E:2808 , HOH E:2873
BINDING SITE FOR RESIDUE SO4 E 2715
39
EC3
SOFTWARE
ASP F:207 , HIS F:229 , ARG F:262 , LYS F:264 , HOH F:2749 , HOH F:2799 , HOH F:2878 , HOH F:2947
BINDING SITE FOR RESIDUE SO4 F 2716
40
EC4
SOFTWARE
ARG E:96 , HIS E:138 , HOH E:2940
BINDING SITE FOR RESIDUE SO4 E 2717
41
EC5
SOFTWARE
ARG C:96 , HIS C:138 , HOH C:2892 , HOH C:2930
BINDING SITE FOR RESIDUE SO4 C 2718
42
EC6
SOFTWARE
ASP A:73 , ARG B:96 , HIS B:138
BINDING SITE FOR RESIDUE GOL B 2001
43
EC7
SOFTWARE
ARG A:96 , TYR A:136 , HIS A:138 , HOH A:2815 , HOH A:2948
BINDING SITE FOR RESIDUE GOL A 2002
44
EC8
SOFTWARE
ARG D:96 , TYR D:136 , HIS D:138 , HOH D:2878 , LYS F:100
BINDING SITE FOR RESIDUE GOL D 2003
45
EC9
SOFTWARE
ARG F:96 , HIS F:138 , HOH F:2824 , HOH F:2904
BINDING SITE FOR RESIDUE GOL F 2004
46
FC1
SOFTWARE
THR E:65 , ASP E:67 , ARG E:96 , MAN E:401 , HOH E:2958
BINDING SITE FOR RESIDUE GOL E 2005
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: POLYGALACTURONASE (A:222-235,B:222-235,C:222-235,D:22...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
POLYGALACTURONASE
PS00502
Polygalacturonase active site.
PGLR1_ASPNG
222-235
6
A:222-235
B:222-235
C:222-235
D:222-235
E:222-235
F:222-235
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1nhca_ (A:)
1b: SCOP_d1nhcb_ (B:)
1c: SCOP_d1nhcc_ (C:)
1d: SCOP_d1nhcd_ (D:)
1e: SCOP_d1nhce_ (E:)
1f: SCOP_d1nhcf_ (F:)
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)
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Single-stranded right-handed beta-helix
(140)
Superfamily
:
Pectin lyase-like
(89)
Family
:
Galacturonase
(11)
Protein domain
:
Polygalacturonase
(9)
Fungus (Aspergillus niger), endo-polygalacturonase I [TaxId: 5061]
(1)
1a
d1nhca_
A:
1b
d1nhcb_
B:
1c
d1nhcc_
C:
1d
d1nhcd_
D:
1e
d1nhce_
E:
1f
d1nhcf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1nhcA00 (A:33-368)
1b: CATH_1nhcB00 (B:33-368)
1c: CATH_1nhcC00 (C:33-368)
1d: CATH_1nhcD00 (D:33-368)
1e: CATH_1nhcE00 (E:33-368)
1f: CATH_1nhcF00 (F:33-368)
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
3 Solenoid
(196)
Topology
:
Pectate Lyase C-like
(105)
Homologous Superfamily
:
Single-stranded right-handed beta-helix, Pectin lyase-like
(73)
Aspergillus niger. Organism_taxid: 5061.
(3)
1a
1nhcA00
A:33-368
1b
1nhcB00
B:33-368
1c
1nhcC00
C:33-368
1d
1nhcD00
D:33-368
1e
1nhcE00
E:33-368
1f
1nhcF00
F:33-368
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_28_1nhcF01 (F:50-368)
1b: PFAM_Glyco_hydro_28_1nhcF02 (F:50-368)
1c: PFAM_Glyco_hydro_28_1nhcF03 (F:50-368)
1d: PFAM_Glyco_hydro_28_1nhcF04 (F:50-368)
1e: PFAM_Glyco_hydro_28_1nhcF05 (F:50-368)
1f: PFAM_Glyco_hydro_28_1nhcF06 (F:50-368)
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Organisms
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Clan
:
Pec_lyase
(42)
Family
:
Glyco_hydro_28
(6)
Aspergillus niger
(1)
1a
Glyco_hydro_28-1nhcF01
F:50-368
1b
Glyco_hydro_28-1nhcF02
F:50-368
1c
Glyco_hydro_28-1nhcF03
F:50-368
1d
Glyco_hydro_28-1nhcF04
F:50-368
1e
Glyco_hydro_28-1nhcF05
F:50-368
1f
Glyco_hydro_28-1nhcF06
F:50-368
[
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