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3IIQ
Biol. Unit 2
Info
Asym.Unit (96 KB)
Biol.Unit 1 (43 KB)
Biol.Unit 2 (43 KB)
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(1)
Title
:
CRYSTALLOGRAPHIC ANALYSIS OF BACTERIAL SIGNAL PEPTIDASE IN TERNARY COMPLEX WITH ARYLOMYCIN A2 AND A BETA-SULTAM INHIBITOR
Authors
:
M. Paetzel
Date
:
03 Aug 09 (Deposition) - 01 Sep 09 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: B,D (1x)
Biol. Unit 2: A,C (1x)
Keywords
:
Ser/Lys Dyad, Lipopeptide, Serine Protease, Biaryl Bridge, Morpholino Beta-Sultam, Antibiotic, Peptidase, Hydrolase-Antibiotic-Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
C. Luo, P. Roussel, J. Dreier, M. G. Page, M. Paetzel
Crystallographic Analysis Of Bacterial Signal Peptidase In Ternary Complex With Arylomycin A2 And A Beta-Sultam Inhibitor.
Biochemistry V. 48 8976 2009
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Hetero Components
(8, 12)
Info
All Hetero Components
1a: (2S)-(4-HYDROXYPHENYL)(METHYLAMINO... (5PGa)
1b: (2S)-(4-HYDROXYPHENYL)(METHYLAMINO... (5PGb)
2a: ACETONITRILE (CCNa)
2b: ACETONITRILE (CCNb)
3a: D-ALANINE (DALa)
3b: D-ALANINE (DALb)
4a: N-METHYL-D-SERINE (DSEa)
4b: N-METHYL-D-SERINE (DSEb)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
6a: 4-[(1,1-DIOXIDO-1,2-THIAZETIDIN-2-... (JZAa)
6b: 4-[(1,1-DIOXIDO-1,2-THIAZETIDIN-2-... (JZAb)
7a: 10-METHYLUNDECANOIC ACID (M12a)
7b: 10-METHYLUNDECANOIC ACID (M12b)
8a: FRAGMENT OF TRITON X-100 (TRTa)
8b: FRAGMENT OF TRITON X-100 (TRTb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5PG
1
Mod. Amino Acid
(2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID
2
CCN
2
Ligand/Ion
ACETONITRILE
3
DAL
1
Mod. Amino Acid
D-ALANINE
4
DSE
1
Mod. Amino Acid
N-METHYL-D-SERINE
5
GOL
4
Ligand/Ion
GLYCEROL
6
JZA
1
Ligand/Ion
4-[(1,1-DIOXIDO-1,2-THIAZETIDIN-2-YL)CARBONYL]MORPHOLINE
7
M12
1
Ligand/Ion
10-METHYLUNDECANOIC ACID
8
TRT
1
Ligand/Ion
FRAGMENT OF TRITON X-100
[
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Sites
(10, 10)
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: BC1 (SOFTWARE)
10: BC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:88 , SER A:90 , ASN A:277 , SER A:278 , ALA A:279 , GLU A:307 , TYR C:6
BINDING SITE FOR RESIDUE JZA A 324
02
AC2
SOFTWARE
GLU A:104 , THR A:297 , GOL A:326
BINDING SITE FOR RESIDUE TRT A 325
03
AC3
SOFTWARE
TRT A:325
BINDING SITE FOR RESIDUE GOL A 326
04
AC4
SOFTWARE
ARG A:236 , GOL A:328 , GOL A:329
BINDING SITE FOR RESIDUE GOL A 327
05
AC5
SOFTWARE
GLY A:321 , ILE A:322 , HIS A:323 , GOL A:327 , CCN A:330 , ASN B:186
BINDING SITE FOR RESIDUE GOL A 328
06
AC6
SOFTWARE
SER A:317 , ARG A:318 , GOL A:327 , HOH A:2127 , HOH A:2128
BINDING SITE FOR RESIDUE GOL A 329
07
AC7
SOFTWARE
THR A:94 , ILE A:322 , HIS A:323 , GOL A:328 , CCN A:331
BINDING SITE FOR RESIDUE CCN A 330
08
AC8
SOFTWARE
THR A:94 , HIS A:235 , ARG A:236 , HIS A:323 , CCN A:330 , HOH A:2079
BINDING SITE FOR RESIDUE CCN A 331
09
BC1
SOFTWARE
PHE A:196 , PHE B:196 , ASP B:276 , ASN B:277 , SER B:278 , ALA B:279 , TYR B:283 , JZA B:324
BINDING SITE FOR RESIDUE TRT B 325
10
BC2
SOFTWARE
GLU A:82 , PRO A:83 , PHE A:84 , GLN A:85 , PRO A:87 , SER A:88 , SER A:90 , ASP A:142 , TYR A:143 , ILE A:144 , LYS A:145 , JZA A:324 , HOH A:2002 , HOH A:2024 , HOH A:2025 , HOH C:2002
BINDING SITE FOR CHAIN C OF ARYLOMYCIN A2
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: SPASE_I_1 (A:88-95)
2: SPASE_I_2 (A:145-157)
3: SPASE_I_3 (A:268-281)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SPASE_I_1
PS00501
Signal peptidases I serine active site.
LEP_ECOLI
89-96
1
A:88-95
-
2
SPASE_I_2
PS00760
Signal peptidases I lysine active site.
LEP_ECOLI
146-158
1
A:145-157
-
3
SPASE_I_3
PS00761
Signal peptidases I signature 3.
LEP_ECOLI
269-282
1
A:268-281
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3iiqa_ (A:)
1b: SCOP_d3iiqb_ (B:)
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Classes
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Protein Domains
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(
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Organisms
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(
)
Class
:
All beta proteins
(24004)
Fold
:
LexA/Signal peptidase
(17)
Superfamily
:
LexA/Signal peptidase
(17)
Family
:
Type 1 signal peptidase
(5)
Protein domain
:
Type 1 signal peptidase
(5)
Escherichia coli [TaxId: 562]
(5)
1a
d3iiqa_
A:
1b
d3iiqb_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3iiqB02 (B:154-188,B:224-262)
1b: CATH_3iiqA02 (A:154-188,A:224-262)
2a: CATH_3iiqA01 (A:79-153,A:263-319)
2b: CATH_3iiqB01 (B:80-153,B:263-323)
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Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Signal Peptidase I; Chain: A, domain 2
(4)
Homologous Superfamily
:
[code=2.170.230.10, no name defined]
(4)
Escherichia coli. Organism_taxid: 83333. Strain: k-12.
(1)
1a
3iiqB02
B:154-188,B:224-262
1b
3iiqA02
A:154-188,A:224-262
Architecture
:
Ribbon
(789)
Topology
:
Umud Fragment, subunit A
(13)
Homologous Superfamily
:
Umud Fragment, subunit A
(13)
Escherichia coli. Organism_taxid: 83333. Strain: k-12.
(1)
2a
3iiqA01
A:79-153,A:263-319
2b
3iiqB01
B:80-153,B:263-323
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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show SS bonds with a radius of 100 units (=0.4Å)
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