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2PNL
Asym. Unit
Info
Asym.Unit (339 KB)
Biol.Unit 1 (39 KB)
Biol.Unit 10 (39 KB)
Biol.Unit 2 (40 KB)
Biol.Unit 3 (40 KB)
Biol.Unit 4 (39 KB)
Biol.Unit 5 (40 KB)
Biol.Unit 6 (38 KB)
Biol.Unit 7 (38 KB)
Biol.Unit 8 (40 KB)
Biol.Unit 9 (39 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF VP4 PROTEASE FROM INFECTIOUS PANCREATIC NECROSIS VIRUS (IPNV) IN SPACE GROUP P1
Authors
:
M. Paetzel, J. Lee, A. R. Feldman, B. Delmas
Date
:
24 Apr 07 (Deposition) - 05 Jun 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.21
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
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)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Biol. Unit 9: I (1x)
Biol. Unit 10: J (1x)
Keywords
:
Acyl-Enzyme, Protease, Ser/Lys Dyad, Viral Protease, Substrate Complex, Product Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Lee, A. R. Feldman, B. Delmas, M. Paetzel
Crystal Structure Of The Vp4 Protease From Infectious Pancreatic Necrosis Virus Reveals The Acyl-Enzyme Complex For An Intermolecular Self-Cleavage Reaction.
J. Biol. Chem. V. 282 24928 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 47)
Info
All Hetero Components
1a: GUANIDINE (GAIa)
1b: GUANIDINE (GAIb)
1c: GUANIDINE (GAIc)
1d: GUANIDINE (GAId)
1e: GUANIDINE (GAIe)
1f: GUANIDINE (GAIf)
1g: GUANIDINE (GAIg)
1h: GUANIDINE (GAIh)
1i: GUANIDINE (GAIi)
1j: GUANIDINE (GAIj)
1k: GUANIDINE (GAIk)
1l: GUANIDINE (GAIl)
1m: GUANIDINE (GAIm)
1n: GUANIDINE (GAIn)
1o: GUANIDINE (GAIo)
1p: GUANIDINE (GAIp)
1q: GUANIDINE (GAIq)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAI
17
Ligand/Ion
GUANIDINE
2
MSE
30
Mod. Amino Acid
SELENOMETHIONINE
[
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]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:524 , ASN A:528 , HIS A:547 , HOH A:2006 , HOH A:2037 , HOH A:2039 , HOH E:2033
BINDING SITE FOR RESIDUE GAI A 2002
02
AC2
SOFTWARE
ASP A:644 , THR A:699 , SER A:700 , ALA A:703
BINDING SITE FOR RESIDUE GAI A 2005
03
AC3
SOFTWARE
PRO B:536 , ASN B:616 , ASN B:618 , HIS H:581 , HOH H:2155
BINDING SITE FOR RESIDUE GAI B 2003
04
AC4
SOFTWARE
SER B:559 , LEU B:610 , GLU B:622 , HOH B:2015 , HOH B:2040
BINDING SITE FOR RESIDUE GAI B 2004
05
AC5
SOFTWARE
LEU B:524 , ASN B:528 , HIS B:547 , PHE B:625 , HOH B:2032 , HOH B:2036 , HOH B:2040 , HOH B:2062
BINDING SITE FOR RESIDUE GAI B 2009
06
AC6
SOFTWARE
SER C:559 , LEU C:610 , GLU C:622 , HOH C:2045 , HOH C:2099
BINDING SITE FOR RESIDUE GAI C 2001
07
AC7
SOFTWARE
LEU C:524 , ASN C:528 , HIS C:547 , HOH C:2019 , HOH C:2099
BINDING SITE FOR RESIDUE GAI C 2006
08
AC8
SOFTWARE
HIS C:581 , PRO H:536 , ASN H:616 , ASN H:618 , HOH H:2075
BINDING SITE FOR RESIDUE GAI C 2014
09
AC9
SOFTWARE
HOH C:2124 , LEU D:524 , ASN D:528 , HIS D:547 , ILE D:624 , HOH D:2016 , HOH D:2035 , HOH D:2051
BINDING SITE FOR RESIDUE GAI D 2010
10
BC1
SOFTWARE
LEU E:524 , ASN E:528 , HIS E:547 , PHE E:557 , HOH E:2016 , HOH E:2018 , HOH E:2044 , HOH E:2104
BINDING SITE FOR RESIDUE GAI E 2007
11
BC2
SOFTWARE
HIS E:581 , PRO J:536 , ASN J:616 , ASN J:618 , HOH J:2026
BINDING SITE FOR RESIDUE GAI E 2015
12
BC3
SOFTWARE
LEU F:524 , ASN F:528 , HIS F:547 , PHE F:557 , PHE F:625 , HOH F:2062
BINDING SITE FOR RESIDUE GAI F 2011
13
BC4
SOFTWARE
LEU H:524 , ASN H:528 , HIS H:547 , PHE H:557 , HOH H:2048 , HOH H:2049 , HOH H:2068 , HOH H:2154
BINDING SITE FOR RESIDUE GAI H 2008
14
BC5
SOFTWARE
PRO H:597 , PHE H:598 , ALA H:659 , ASP H:660 , HOH H:2134
BINDING SITE FOR RESIDUE GAI H 2016
15
BC6
SOFTWARE
ARG H:715 , ALA H:716 , VAL I:546 , CYS I:669
BINDING SITE FOR RESIDUE GAI H 2017
16
BC7
SOFTWARE
LEU I:524 , ASN I:528 , HIS I:547 , PHE I:557 , PHE I:625 , HOH I:2022 , HOH I:2027 , HOH I:2028 , HOH I:2080
BINDING SITE FOR RESIDUE GAI I 2012
17
BC8
SOFTWARE
LEU J:524 , ASN J:528 , HIS J:547 , HOH J:2060 , HOH J:2064
BINDING SITE FOR RESIDUE GAI J 2013
[
close Site info
]
SAPs(SNPs)/Variants
(2, 20)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_POLS_IPNVS_027 (P565R, chain A/B/C/D/E/F/G/H/I/J, )
2: VAR_POLS_IPNVS_028 (D672A, chain A/B/C/D/E/F/G/H/I/J, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_POLS_IPNVS_027
*
P
565
R
POLS_IPNVS
---
---
A/B/C/D/E/F/G/H/I/J
P
565
R
2
UniProt
VAR_POLS_IPNVS_028
*
D
672
A
POLS_IPNVS
---
---
A/B/C/D/E/F/G/H/I/J
D
672
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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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
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(1, 10)
Info
all PFAM domains
1a: PFAM_Birna_VP4_2pnlJ01 (J:514-706)
1b: PFAM_Birna_VP4_2pnlJ02 (J:514-706)
1c: PFAM_Birna_VP4_2pnlJ03 (J:514-706)
1d: PFAM_Birna_VP4_2pnlJ04 (J:514-706)
1e: PFAM_Birna_VP4_2pnlJ05 (J:514-706)
1f: PFAM_Birna_VP4_2pnlJ06 (J:514-706)
1g: PFAM_Birna_VP4_2pnlJ07 (J:514-706)
1h: PFAM_Birna_VP4_2pnlJ08 (J:514-706)
1i: PFAM_Birna_VP4_2pnlJ09 (J:514-706)
1j: PFAM_Birna_VP4_2pnlJ10 (J:514-706)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Birna_VP4]
(2)
Family
:
Birna_VP4
(2)
Infectious pancreatic necrosis virus (strain Sp) (IPNV)
(2)
1a
Birna_VP4-2pnlJ01
J:514-706
1b
Birna_VP4-2pnlJ02
J:514-706
1c
Birna_VP4-2pnlJ03
J:514-706
1d
Birna_VP4-2pnlJ04
J:514-706
1e
Birna_VP4-2pnlJ05
J:514-706
1f
Birna_VP4-2pnlJ06
J:514-706
1g
Birna_VP4-2pnlJ07
J:514-706
1h
Birna_VP4-2pnlJ08
J:514-706
1i
Birna_VP4-2pnlJ09
J:514-706
1j
Birna_VP4-2pnlJ10
J:514-706
[
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Asym.Unit (339 KB)
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