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2IRV
Biol. Unit 2
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
[
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Hetero Components
(4, 19)
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
13
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
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: BC1 (SOFTWARE)
10: BC2 (SOFTWARE)
11: BC3 (SOFTWARE)
12: BC4 (SOFTWARE)
13: BC5 (SOFTWARE)
14: BC7 (SOFTWARE)
15: BC8 (SOFTWARE)
16: BC9 (SOFTWARE)
17: CC1 (SOFTWARE)
View:
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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
AC8
SOFTWARE
TRP B:241 , LMT B:3888
BINDING SITE FOR RESIDUE LDA B 3840
08
AC9
SOFTWARE
HOH B:61 , TRP B:241 , PHE B:242
BINDING SITE FOR RESIDUE LDA B 3841
09
BC1
SOFTWARE
GLY A:94 , PRO A:95 , TRP A:98 , VAL A:99 , LDA B:3834
BINDING SITE FOR RESIDUE LDA A 3842
10
BC2
SOFTWARE
LDA B:3844
BINDING SITE FOR RESIDUE LDA B 3843
11
BC3
SOFTWARE
LDA B:3843
BINDING SITE FOR RESIDUE LDA B 3844
12
BC4
SOFTWARE
LDA B:3836 , LDA B:3839
BINDING SITE FOR RESIDUE LDA A 3845
13
BC5
SOFTWARE
PHE A:242 , TRP B:212 , ILE B:230 , ILE B:231 , PO4 B:5156
BINDING SITE FOR RESIDUE LDA B 3847
14
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
15
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
16
BC9
SOFTWARE
LEU B:229 , PHE B:232
BINDING SITE FOR RESIDUE PGV B 5138
17
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 only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
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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_d2irva_ (A:)
1b: SCOP_d2irvb_ (B:)
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Protein Domains
(
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(
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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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Atom Selection
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Protein
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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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'
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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)
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show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
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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