PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2IQ7
Asym. Unit
Info
Asym.Unit (400 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (65 KB)
Biol.Unit 4 (63 KB)
Biol.Unit 5 (65 KB)
Biol.Unit 6 (62 KB)
Biol.Unit 7 (60 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE POLYGALACTURONASE FROM COLLETOTRICHUM LUPINI AND ITS IMPLICATIONS FOR THE INTERACTION WITH POLYGALACTURONASE-INHIBITING PROTEINS
Authors
:
D. Bonivento, L. Federici, A. D. Matteo
Date
:
13 Oct 06 (Deposition) - 23 Oct 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.94
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
#
,I
#
,L
#
,M
#
,N
#
,O
#
,Q
#
Biol. Unit 1: A,H
#
(1x)
Biol. Unit 2: B,I
#
(1x)
Biol. Unit 3: C,L
#
(1x)
Biol. Unit 4: D,M
#
(1x)
Biol. Unit 5: E,N
#
(1x)
Biol. Unit 6: F,O
#
(1x)
Biol. Unit 7: G,Q
#
(1x)
(
#
: chains that contain no standard or modified protein/DNA/RNA residue)
Keywords
:
Parallel Beta Helix, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Bonivento, D. Pontiggia, A. D. Matteo, J. Fernandez-Recio, G. Salvi, D. Tsernoglou, F. Cervone, G. D. Lorenzo, L. Federici
Crystal Structure Of The Endopolygalacturonase From The Phytopathogenic Fungus Colletotrichum Lupini And Its Interaction With Polygalacturonase-Inhibiting Proteins
Proteins V. 70 294 2008
[
close entry info
]
Hetero Components
(5, 28)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
5a: TETRAETHYLENE GLYCOL (PG4a)
5b: TETRAETHYLENE GLYCOL (PG4b)
5c: TETRAETHYLENE GLYCOL (PG4c)
5d: TETRAETHYLENE GLYCOL (PG4d)
5e: TETRAETHYLENE GLYCOL (PG4e)
5f: TETRAETHYLENE GLYCOL (PG4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
1
Ligand/Ion
ACETIC ACID
2
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PG4
6
Ligand/Ion
TETRAETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(28, 28)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:156 , GLY A:187 , TYR A:189 , ASN A:209 , PG4 E:3001 , NAG H:364 , HOH H:372
BINDING SITE FOR RESIDUE NAG H 363
02
AC2
SOFTWARE
THR A:156 , TYR A:160 , TYR A:189 , HOH A:3115 , ASN E:334 , PG4 E:3001 , HOH E:3298 , NAG H:363 , MAN H:365 , HOH H:373 , HOH H:379 , HOH H:384 , HOH H:386
BINDING SITE FOR RESIDUE NAG H 364
03
AC3
SOFTWARE
ASN E:334 , TRP E:335 , SER E:356 , GLY E:357 , PG4 E:3001 , NAG H:364 , MAN H:366 , MAN H:367 , HOH H:371 , HOH H:375 , HOH H:381 , HOH H:382
BINDING SITE FOR RESIDUE MAN H 365
04
AC4
SOFTWARE
LYS E:336 , GLY E:357 , SER E:358 , MAN H:365 , MAN H:368 , HOH H:370 , HOH H:385
BINDING SITE FOR RESIDUE MAN H 366
05
AC5
SOFTWARE
ASN A:92 , SER E:356 , GLY E:357 , HOH E:3367 , MAN H:365 , HOH H:377
BINDING SITE FOR RESIDUE MAN H 367
06
AC6
SOFTWARE
TRP E:337 , SER E:338 , SER E:358 , MAN H:366 , HOH H:380 , HOH H:387
BINDING SITE FOR RESIDUE MAN H 368
07
AC7
SOFTWARE
THR B:156 , GLY B:187 , ASN B:209 , HOH G:400 , NAG I:364 , HOH I:365 , HOH I:366 , HOH I:367 , HOH I:370
BINDING SITE FOR RESIDUE NAG I 363
08
AC8
SOFTWARE
TYR B:160 , HOH B:3270 , SER G:232 , NAG I:363 , HOH I:367 , HOH I:368 , HOH I:370
BINDING SITE FOR RESIDUE NAG I 364
09
AC9
SOFTWARE
GLY C:187 , ASN C:209 , HOH C:3030 , NAG L:364 , HOH L:365 , HOH L:366
BINDING SITE FOR RESIDUE NAG L 363
10
BC1
SOFTWARE
TYR C:160 , TYR C:189 , NAG L:363 , HOH L:367 , HOH L:368
BINDING SITE FOR RESIDUE NAG L 364
11
BC2
SOFTWARE
HOH C:3342 , THR D:156 , GLY D:187 , TYR D:189 , ASN D:209 , HOH D:3056 , NAG M:364 , HOH M:365 , HOH M:367 , HOH M:369
BINDING SITE FOR RESIDUE NAG M 363
12
BC3
SOFTWARE
TYR D:189 , HOH D:3204 , NAG M:363 , HOH M:366 , HOH M:368 , HOH M:369
BINDING SITE FOR RESIDUE NAG M 364
13
BC4
SOFTWARE
THR E:156 , GLY E:187 , TYR E:189 , ASN E:209 , HOH E:3123 , NAG N:364 , HOH N:365 , HOH N:366 , HOH N:370 , HOH N:372
BINDING SITE FOR RESIDUE NAG N 363
14
BC5
SOFTWARE
LYS A:336 , HOH E:3060 , NAG N:363 , HOH N:367 , HOH N:368 , HOH N:370 , HOH N:371
BINDING SITE FOR RESIDUE NAG N 364
15
BC6
SOFTWARE
THR F:156 , GLY F:187 , TYR F:189 , ASN F:209 , HOH F:3095 , NAG O:364 , HOH O:365 , HOH O:366 , HOH O:367
BINDING SITE FOR RESIDUE NAG O 363
16
BC7
SOFTWARE
TYR F:160 , NAG O:363
BINDING SITE FOR RESIDUE NAG O 364
17
BC8
SOFTWARE
GLY G:187 , ASN G:209 , NAG Q:364 , HOH Q:365
BINDING SITE FOR RESIDUE NAG Q 363
18
BC9
SOFTWARE
HOH B:3079 , TYR G:160 , TYR G:189 , NAG Q:363 , HOH Q:365 , HOH Q:366
BINDING SITE FOR RESIDUE NAG Q 364
19
CC1
SOFTWARE
SER E:266 , GLY E:267 , THR E:305 , GLY E:306 , THR E:308 , ASN E:334 , HOH E:3229 , HOH E:3236 , HOH E:3250 , HOH E:3296 , HOH E:3298 , NAG H:363 , NAG H:364 , MAN H:365
BINDING SITE FOR RESIDUE PG4 E 3001
20
CC2
SOFTWARE
LYS C:137 , TYR C:160 , LYS C:347 , SER C:348 , HOH C:3245
BINDING SITE FOR RESIDUE PG4 C 3002
21
CC3
SOFTWARE
LYS A:347 , SER A:348 , ASN B:94 , ASN B:135 , LYS B:137
BINDING SITE FOR RESIDUE PG4 B 3003
22
CC4
SOFTWARE
THR A:121 , HOH A:3273 , LEU C:307 , THR C:308 , ASN C:334 , LYS C:336
BINDING SITE FOR RESIDUE PG4 A 3004
23
CC5
SOFTWARE
GLU C:82 , ASN C:117 , GLY C:118 , HOH C:3303 , HOH C:3369 , TYR F:78 , ARG F:109 , HOH F:3261 , HOH F:3289
BINDING SITE FOR RESIDUE PG4 F 3005
24
CC6
SOFTWARE
GLY D:215 , ASN D:243 , LYS D:245 , THR D:274 , HOH D:3180
BINDING SITE FOR RESIDUE PG4 D 3006
25
CC7
SOFTWARE
GLY E:263 , ASN E:300 , GLY E:301 , HOH E:3374 , TYR F:127 , HIS F:129 , ASN F:152 , PEG F:3009 , HOH F:3253
BINDING SITE FOR RESIDUE PEG E 3007
26
CC8
SOFTWARE
ASN B:300 , GLY B:301 , HOH B:3195 , HOH B:3315 , SER E:113 , HIS E:175
BINDING SITE FOR RESIDUE PEG B 3008
27
CC9
SOFTWARE
PEG E:3007 , LYS F:124 , TYR F:127 , GLN F:147 , SER F:150 , ASP F:181
BINDING SITE FOR RESIDUE PEG F 3009
28
DC1
SOFTWARE
LYS B:245 , VAL B:247 , SER B:276 , HOH B:3292 , LYS C:245 , VAL C:247 , SER C:276
BINDING SITE FOR RESIDUE ACY B 3010
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(1, 7)
Info
All SCOP Domains
1a: SCOP_d2iq7a_ (A:)
1b: SCOP_d2iq7b_ (B:)
1c: SCOP_d2iq7c_ (C:)
1d: SCOP_d2iq7d_ (D:)
1e: SCOP_d2iq7e_ (E:)
1f: SCOP_d2iq7f_ (F:)
1g: SCOP_d2iq7g_ (G:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
automated matches
(1)
Colletotrichum lupini [TaxId: 145971]
(1)
1a
d2iq7a_
A:
1b
d2iq7b_
B:
1c
d2iq7c_
C:
1d
d2iq7d_
D:
1e
d2iq7e_
E:
1f
d2iq7f_
F:
1g
d2iq7g_
G:
[
close SCOP info
]
CATH Domains
(1, 7)
Info
all CATH domains
1a: CATH_2iq7A00 (A:24-362)
1b: CATH_2iq7B00 (B:24-362)
1c: CATH_2iq7C00 (C:24-362)
1d: CATH_2iq7D00 (D:24-362)
1e: CATH_2iq7E00 (E:24-362)
1f: CATH_2iq7G00 (G:24-362)
1g: CATH_2iq7F00 (F:25-362)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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)
Colletotrichum lupini. Organism_taxid: 145971
(1)
1a
2iq7A00
A:24-362
1b
2iq7B00
B:24-362
1c
2iq7C00
C:24-362
1d
2iq7D00
D:24-362
1e
2iq7E00
E:24-362
1f
2iq7G00
G:24-362
1g
2iq7F00
F:25-362
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (400 KB)
Header - Asym.Unit
Biol.Unit 1 (65 KB)
Header - Biol.Unit 1
Biol.Unit 2 (64 KB)
Header - Biol.Unit 2
Biol.Unit 3 (65 KB)
Header - Biol.Unit 3
Biol.Unit 4 (63 KB)
Header - Biol.Unit 4
Biol.Unit 5 (65 KB)
Header - Biol.Unit 5
Biol.Unit 6 (62 KB)
Header - Biol.Unit 6
Biol.Unit 7 (60 KB)
Header - Biol.Unit 7
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2IQ7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
