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3BS6
Biol. Unit 1
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Asym.Unit (101 KB)
Biol.Unit 1 (48 KB)
Biol.Unit 2 (50 KB)
Biol.Unit 3 (184 KB)
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Title
:
1.8 ANGSTROM CRYSTAL STRUCTURE OF THE PERIPLASMIC DOMAIN OF THE MEMBRANE INSERTASE YIDC
Authors
:
S. Ravaud, I. Sinning
Date
:
22 Dec 07 (Deposition) - 12 Feb 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (2x)
Keywords
:
Yidc/Oxa1/Alb3 Family, Membrane Insertion, Chaperone, Sec Translocon, Periplasmic Domain, Beta Supersandwich Fold, Helical Linker Domain, Membrane Protein, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Ravaud, G. Stjepanovic, K. Wild, I. Sinning
The Crystal Structure Of The Periplasmic Domain Of The Escherichia Coli Membrane Protein Insertase Yidc Contains A Substrate Binding Cleft
J. Biol. Chem. V. 283 9350 2008
(for further references see the
PDB file header
)
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: NONAETHYLENE GLYCOL (2PEa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
5a: TETRAETHYLENE GLYCOL (PG4a)
6a: TRIETHYLENE GLYCOL (PGEa)
6b: TRIETHYLENE GLYCOL (PGEb)
6c: TRIETHYLENE GLYCOL (PGEc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2PE
-1
Ligand/Ion
NONAETHYLENE GLYCOL
2
CA
-1
Ligand/Ion
CALCIUM ION
3
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
4
MSE
4
Mod. Amino Acid
SELENOMETHIONINE
5
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
6
PGE
2
Ligand/Ion
TRIETHYLENE GLYCOL
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Sites
(12, 12)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:230 , GLU A:231 , HOH A:343 , HOH A:354 , GLU B:228 , TYR B:230 , GLU B:231
BINDING SITE FOR RESIDUE CA A 1
02
AC2
SOFTWARE
GLU A:231 , HOH A:485 , GLU B:228 , GLU B:231 , HOH B:516
BINDING SITE FOR RESIDUE CA A 2
03
AC3
SOFTWARE
GLU A:228 , GLU B:231 , LYS B:232 , HOH B:416 , HOH B:589
BINDING SITE FOR RESIDUE CA A 3
04
AC4
SOFTWARE
ASN A:125 , HOH A:476 , ALA B:124 , HOH B:392
BINDING SITE FOR RESIDUE CA A 4
05
AC5
SOFTWARE
ALA A:124 , HOH A:370 , HOH A:378 , ASN B:125
BINDING SITE FOR RESIDUE CA A 5
06
AC6
SOFTWARE
PHE A:193 , GLN A:195 , ASN A:273 , LYS A:289 , 2PE B:1
BINDING SITE FOR RESIDUE PG4 A 336
07
AC7
SOFTWARE
HIS A:267 , THR A:300 , GLY A:301 , ALA A:302 , MSE A:303 , ASN A:304 , EDO A:340 , HOH A:382 , HOH A:496 , HOH A:515 , HOH A:539 , GLY B:143 , ASN B:145
BINDING SITE FOR RESIDUE PGE A 337
08
AC8
SOFTWARE
GLU A:146 , GLN A:148 , ASN A:177 , ASN A:304 , HOH A:453 , HOH A:465 , HOH A:508 , ASN B:145 , GLU B:146 , LYS B:168 , ARG B:169 , HOH B:518
BINDING SITE FOR RESIDUE PGE A 338
09
AC9
SOFTWARE
LYS A:64 , HOH A:510
BINDING SITE FOR RESIDUE EDO A 339
10
BC1
SOFTWARE
SER A:192 , ASN A:268 , SER A:290 , MSE A:303 , ASN A:304 , PGE A:337 , HOH A:515 , HOH A:555
BINDING SITE FOR RESIDUE EDO A 340
11
BC2
SOFTWARE
ASP A:315 , HOH A:361 , HOH A:520
BINDING SITE FOR RESIDUE EDO A 7
12
BC3
SOFTWARE
PG4 A:336 , GLN B:111 , ARG B:128 , PHE B:193 , ASN B:245 , THR B:271 , ASN B:273 , TYR B:275 , LYS B:289 , SER B:290 , GLN B:291 , HOH B:549 , HOH B:587 , HOH B:614
BINDING SITE FOR RESIDUE 2PE B 1
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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SCOP Domains
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (101 KB)
Header - Asym.Unit
Biol.Unit 1 (48 KB)
Header - Biol.Unit 1
Biol.Unit 2 (50 KB)
Header - Biol.Unit 2
Biol.Unit 3 (184 KB)
Header - Biol.Unit 3
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