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Biol. Unit 2
Info
Asym.Unit (123 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (55 KB)
Biol.Unit 3 (115 KB)
Biol.Unit 4 (114 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE RHODOPSIN
Authors
:
D. C. Teller, T. Okada, C. A. Behnke, K. Palczewski, R. E. Stenkamp
Date
:
26 Jan 01 (Deposition) - 04 Jul 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Biol. Unit 4: A,B (1x)
Keywords
:
Signaling Protein, G-Protein-Coupled Receptors, Membrane Protein Photoreceptor Cells, Phototransduction
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. C. Teller, T. Okada, C. A. Behnke, K. Palczewski, R. E. Stenkamp
Advances In Determination Of A High-Resolution Three-Dimensional Structure Of Rhodopsin, A Model Of G-Protein-Coupled Receptors (Gpcrs).
Biochemistry V. 40 7761 2001
[
close entry info
]
Hetero Components
(7, 13)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
3a: B-NONYLGLUCOSIDE (BNGa)
3b: B-NONYLGLUCOSIDE (BNGb)
3c: B-NONYLGLUCOSIDE (BNGc)
3d: B-NONYLGLUCOSIDE (BNGd)
3e: B-NONYLGLUCOSIDE (BNGe)
3f: B-NONYLGLUCOSIDE (BNGf)
3g: B-NONYLGLUCOSIDE (BNGg)
4a: MERCURY (II) ION (HGa)
4b: MERCURY (II) ION (HGb)
4c: MERCURY (II) ION (HGc)
4d: MERCURY (II) ION (HGd)
4e: MERCURY (II) ION (HGe)
4f: MERCURY (II) ION (HGf)
5a: HEPTANE-1,2,3-TRIOL (HTOa)
5b: HEPTANE-1,2,3-TRIOL (HTOb)
5c: HEPTANE-1,2,3-TRIOL (HTOc)
5d: HEPTANE-1,2,3-TRIOL (HTOd)
5e: HEPTANE-1,2,3-TRIOL (HTOe)
5f: HEPTANE-1,2,3-TRIOL (HTOf)
6a: ALPHA-D-MANNOSE (MANa)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
8a: PALMITIC ACID (PLMa)
8b: PALMITIC ACID (PLMb)
8c: PALMITIC ACID (PLMc)
9a: RETINAL (RETa)
9b: RETINAL (RETb)
10a: ZINC ION (ZNa)
10b: ZINC ION (ZNb)
10c: ZINC ION (ZNc)
10d: ZINC ION (ZNd)
10e: ZINC ION (ZNe)
10f: ZINC ION (ZNf)
10g: ZINC ION (ZNg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
1
Mod. Amino Acid
ACETYL GROUP
2
BMA
2
Ligand/Ion
BETA-D-MANNOSE
3
BNG
2
Ligand/Ion
B-NONYLGLUCOSIDE
4
HG
-1
Ligand/Ion
MERCURY (II) ION
5
HTO
2
Ligand/Ion
HEPTANE-1,2,3-TRIOL
6
MAN
-1
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
PLM
1
Ligand/Ion
PALMITIC ACID
9
RET
1
Ligand/Ion
RETINAL
10
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
11: BC3 (SOFTWARE)
12: BC4 (SOFTWARE)
13: BC5 (SOFTWARE)
14: BC9 (SOFTWARE)
15: CC2 (SOFTWARE)
16: CC4 (SOFTWARE)
17: CC6 (SOFTWARE)
18: CC7 (SOFTWARE)
19: CC8 (SOFTWARE)
20: CC9 (SOFTWARE)
21: DC1 (SOFTWARE)
22: DC3 (SOFTWARE)
23: DC5 (SOFTWARE)
24: DC6 (SOFTWARE)
25: DC7 (SOFTWARE)
26: DC9 (SOFTWARE)
27: EC2 (SOFTWARE)
28: EC5 (SOFTWARE)
29: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAG A:504 , LYS B:16
BINDING SITE FOR RESIDUE MAN A 503
02
AC2
SOFTWARE
MAN A:503 , NAG A:505 , LYS B:16
BINDING SITE FOR RESIDUE NAG A 504
03
AC3
SOFTWARE
THR A:4 , ASN A:15 , GLY A:18 , VAL A:20 , NAG A:504 , NAG B:605
BINDING SITE FOR RESIDUE NAG A 505
04
AC4
SOFTWARE
BMA B:603
BINDING SITE FOR RESIDUE BMA B 602
05
AC5
SOFTWARE
LYS A:16 , BMA B:602 , NAG B:604
BINDING SITE FOR RESIDUE BMA B 603
06
AC6
SOFTWARE
LYS A:16 , BMA B:603 , NAG B:605
BINDING SITE FOR RESIDUE NAG B 604
07
AC7
SOFTWARE
NAG A:505 , THR B:4 , ASN B:15 , GLY B:18 , VAL B:20 , NAG B:604
BINDING SITE FOR RESIDUE NAG B 605
08
AC8
SOFTWARE
NAG A:705 , GLU B:197
BINDING SITE FOR RESIDUE NAG A 704
09
BC1
SOFTWARE
NAG B:805
BINDING SITE FOR RESIDUE NAG B 804
10
BC2
SOFTWARE
PRO A:7 , MET B:1 , ASN B:2 , GLY B:280 , SER B:281 , ASP B:282 , NAG B:804
BINDING SITE FOR RESIDUE NAG B 805
11
BC3
SOFTWARE
ALA A:234 , ALA A:235 , ARG A:252 , ILE A:305 , MET A:308 , TRP B:35 , SER B:38 , MET B:39
BINDING SITE FOR RESIDUE BNG A 1500
12
BC4
SOFTWARE
GLU A:232 , ARG A:252 , ILE A:256 , TRP B:35 , BNG B:1502
BINDING SITE FOR RESIDUE BNG A 1501
13
BC5
SOFTWARE
BNG A:1501 , TRP B:35
BINDING SITE FOR RESIDUE BNG B 1502
14
BC9
SOFTWARE
TYR B:274 , PHE B:283 , GLY B:284 , PRO B:285 , PHE B:287
BINDING SITE FOR RESIDUE BNG B 1506
15
CC2
SOFTWARE
ALA B:260 , CYS B:264 , THR B:297
BINDING SITE FOR RESIDUE HG B 902
16
CC4
SOFTWARE
ALA B:132 , CYS B:222 , TYR B:223 , LEU B:226
BINDING SITE FOR RESIDUE HG B 904
17
CC6
SOFTWARE
HIS B:65 , LYS B:67 , CYS B:316
BINDING SITE FOR RESIDUE HG B 906
18
CC7
SOFTWARE
PRO B:7 , HIS B:195
BINDING SITE FOR RESIDUE ZN B 956
19
CC8
SOFTWARE
GLU A:201 , GLN A:279 , GLU B:196
BINDING SITE FOR RESIDUE ZN A 957
20
CC9
SOFTWARE
GLU A:196 , GLU B:201 , GLN B:279
BINDING SITE FOR RESIDUE ZN B 958
21
DC1
SOFTWARE
LYS A:311 , ARG A:314 , ASN A:315 , GLY A:329 , ASP A:330 , HIS B:100
BINDING SITE FOR RESIDUE ZN A 959
22
DC3
SOFTWARE
GLU B:122 , TRP B:126 , MET B:163 , ALA B:164 , CYS B:167 , HIS B:211
BINDING SITE FOR RESIDUE ZN B 963
23
DC5
SOFTWARE
LEU A:321 , CYS A:322 , PLM A:1323 , MET B:49 , PHE B:88
BINDING SITE FOR RESIDUE PLM A 1322
24
DC6
SOFTWARE
CYS A:323 , PLM A:1322 , VAL B:81 , PHE B:85
BINDING SITE FOR RESIDUE PLM A 1323
25
DC7
SOFTWARE
MET A:49 , CYS B:322
BINDING SITE FOR RESIDUE PLM B 1322
26
DC9
SOFTWARE
GLU B:113 , ALA B:117 , THR B:118 , GLY B:121 , GLU B:122 , CYS B:187 , MET B:207 , HIS B:211 , PHE B:212 , PHE B:261 , TRP B:265 , TYR B:268 , ALA B:292 , LYS B:296
BINDING SITE FOR RESIDUE RET B 1296
27
EC2
SOFTWARE
SER A:38 , ALA A:42 , MET B:308 , ARG B:314
BINDING SITE FOR RESIDUE HTO B 1401
28
EC5
SOFTWARE
MET A:317 , LEU A:328 , PHE B:45 , ILE B:48 , THR B:92 , LEU B:95 , TYR B:96
BINDING SITE FOR RESIDUE HTO A 1405
29
EC6
SOFTWARE
VAL B:300 , TYR B:301 , VAL B:304 , ILE B:305
BINDING SITE FOR RESIDUE HTO B 1406
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: G_PROTEIN_RECEP_F1_1 (B:123-139)
2: OPSIN (B:290-306)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
G_PROTEIN_RECEP_F1_1
PS00237
G-protein coupled receptors family 1 signature.
OPSD_BOVIN
123-139
1
-
B:123-139
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_BOVIN
290-306
1
-
B:290-306
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1hzxa_ (A:)
1b: SCOP_d1hzxb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Family A G protein-coupled receptor-like
(138)
Superfamily
:
Family A G protein-coupled receptor-like
(138)
Family
:
Rhodopsin-like
(16)
Protein domain
:
Rhodopsin
(8)
Cow (Bos taurus) [TaxId: 9913]
(8)
1a
d1hzxa_
A:
1b
d1hzxb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1hzxB00 (B:1-326)
1b: CATH_1hzxA00 (A:1-348)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Homologous Superfamily
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Cattle (Bos taurus)
(9)
1a
1hzxB00
B:1-326
1b
1hzxA00
A:1-348
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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Asym.Unit (123 KB)
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