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2IRV
Asym. Unit
Info
Asym.Unit (71 KB)
Biol.Unit 1 (31 KB)
Biol.Unit 2 (36 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLPG, A RHOMBOID INTRAMEMBRANE SERINE PROTEASE
Authors
:
E. Bibi, D. Fass, A. Ben-Shem
Date
:
16 Oct 06 (Deposition) - 31 Oct 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Membrane Protein, Cavity, Ser-His Dyad
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Ben-Shem, D. Fass, E. Bibi
Structural Basis For Intramembrane Proteolysis By Rhomboid Serine Proteases.
Proc. Natl. Acad. Sci. Usa V. 104 462 2007
[
close entry info
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Hetero Components
(4, 22)
Info
All Hetero Components
1a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
1b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
1c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
1d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
1e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
1f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
1g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
1h: LAURYL DIMETHYLAMINE-N-OXIDE (LDAh)
1i: LAURYL DIMETHYLAMINE-N-OXIDE (LDAi)
1j: LAURYL DIMETHYLAMINE-N-OXIDE (LDAj)
1k: LAURYL DIMETHYLAMINE-N-OXIDE (LDAk)
1l: LAURYL DIMETHYLAMINE-N-OXIDE (LDAl)
1m: LAURYL DIMETHYLAMINE-N-OXIDE (LDAm)
1n: LAURYL DIMETHYLAMINE-N-OXIDE (LDAn)
1o: LAURYL DIMETHYLAMINE-N-OXIDE (LDAo)
1p: LAURYL DIMETHYLAMINE-N-OXIDE (LDAp)
2a: DODECYL-BETA-D-MALTOSIDE (LMTa)
3a: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVa)
3b: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVb)
3c: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVc)
3d: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVd)
4a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LDA
16
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
2
LMT
1
Ligand/Ion
DODECYL-BETA-D-MALTOSIDE
3
PGV
4
Ligand/Ion
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
4
PO4
1
Ligand/Ion
PHOSPHATE ION
[
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Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH B:14 , TRP B:212 , ARG B:227 , GLY B:228 , ILE B:230 , LDA B:3847
BINDING SITE FOR RESIDUE PO4 B 5156
02
AC2
SOFTWARE
LDA A:3842 , HOH B:69 , VAL B:106 , ILE B:113 , LEU B:114
BINDING SITE FOR RESIDUE LDA B 3834
03
AC3
SOFTWARE
VAL A:106 , TRP B:98 , ILE B:102 , LDA B:3836
BINDING SITE FOR RESIDUE LDA B 3835
04
AC4
SOFTWARE
LDA A:3845 , PRO B:95 , ILE B:102 , LDA B:3835
BINDING SITE FOR RESIDUE LDA B 3836
05
AC5
SOFTWARE
MET B:101 , PHE B:108 , LEU B:148 , LEU B:155 , LEU B:156 , TRP B:159
BINDING SITE FOR RESIDUE LDA B 3837
06
AC6
SOFTWARE
VAL B:96 , SER B:171
BINDING SITE FOR RESIDUE LDA B 3838
07
AC7
SOFTWARE
LDA A:3845
BINDING SITE FOR RESIDUE LDA B 3839
08
AC8
SOFTWARE
TRP B:241 , LMT B:3888
BINDING SITE FOR RESIDUE LDA B 3840
09
AC9
SOFTWARE
HOH B:61 , TRP B:241 , PHE B:242
BINDING SITE FOR RESIDUE LDA B 3841
10
BC1
SOFTWARE
GLY A:94 , PRO A:95 , TRP A:98 , VAL A:99 , LDA B:3834
BINDING SITE FOR RESIDUE LDA A 3842
11
BC2
SOFTWARE
LDA B:3844
BINDING SITE FOR RESIDUE LDA B 3843
12
BC3
SOFTWARE
LDA B:3843
BINDING SITE FOR RESIDUE LDA B 3844
13
BC4
SOFTWARE
LDA B:3836 , LDA B:3839
BINDING SITE FOR RESIDUE LDA A 3845
14
BC5
SOFTWARE
PHE A:242 , TRP B:212 , ILE B:230 , ILE B:231 , PO4 B:5156
BINDING SITE FOR RESIDUE LDA B 3847
15
BC6
SOFTWARE
TRP A:159 , TYR A:160
BINDING SITE FOR RESIDUE LDA A 3850
16
BC7
SOFTWARE
HOH B:32 , HOH B:47 , HOH B:63 , LEU B:184 , PHE B:192 , SER B:193 , SER B:248 , MET B:249 , GLY B:252 , ALA B:256 , LDA B:3840
BINDING SITE FOR RESIDUE LMT B 3888
17
BC8
SOFTWARE
HOH B:18 , HOH B:78 , HIS B:150 , PHE B:153 , ASN B:154 , TRP B:157 , SER B:201 , TYR B:205 , PHE B:232 , TRP B:236 , HIS B:254
BINDING SITE FOR RESIDUE PGV B 5136
18
BC9
SOFTWARE
LEU B:229 , PHE B:232
BINDING SITE FOR RESIDUE PGV B 5138
19
CC1
SOFTWARE
TRP B:236
BINDING SITE FOR RESIDUE PGV B 5139
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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Sorry, no Info available
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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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2irva_ (A:)
1b: SCOP_d2irvb_ (B:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Rhomboid-like
(22)
Superfamily
:
Rhomboid-like
(22)
Family
:
Rhomboid-like
(22)
Protein domain
:
GlpG
(19)
Escherichia coli [TaxId: 562]
(19)
1a
d2irva_
A:
1b
d2irvb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2irvB00 (B:93-271)
1b: CATH_2irvA00 (A:92-273)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Rhomboid-like fold
(7)
Homologous Superfamily
:
Rhomboid-like domains
(7)
Escherichia coli k12. Organism_taxid: 83333. Strain: k12.
(1)
1a
2irvB00
B:93-271
1b
2irvA00
A:92-273
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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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)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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Asym.Unit (71 KB)
Header - Asym.Unit
Biol.Unit 1 (31 KB)
Header - Biol.Unit 1
Biol.Unit 2 (36 KB)
Header - Biol.Unit 2
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