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2HPY
Biol. Unit 2
Info
Asym.Unit (131 KB)
Biol.Unit 1 (122 KB)
Biol.Unit 2 (123 KB)
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(1)
Title
:
CRYSTALLOGRAPHIC MODEL OF LUMIRHODOPSIN
Authors
:
H. Nakamichi, T. Okada
Date
:
18 Jul 06 (Deposition) - 22 Aug 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (1x)
Keywords
:
G Protein-Coupled Receptor, Visual Pigment, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Nakamichi, T. Okada
Local Peptide Movement In The Photoreaction Intermediate Of Rhodopsin
Proc. Natl. Acad. Sci. Usa V. 103 12729 2006
[
close entry info
]
Hetero Components
(7, 14)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
3a: MERCURY (II) ION (HGa)
3b: MERCURY (II) ION (HGb)
3c: MERCURY (II) ION (HGc)
3d: MERCURY (II) ION (HGd)
3e: MERCURY (II) ION (HGe)
3f: MERCURY (II) ION (HGf)
4a: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGa)
4b: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGb)
4c: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGc)
4d: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGd)
5a: HEPTANE-1,2,3-TRIOL (HTOa)
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)
8d: PALMITIC ACID (PLMd)
8e: PALMITIC ACID (PLMe)
8f: PALMITIC ACID (PLMf)
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
HG
-1
Ligand/Ion
MERCURY (II) ION
4
HTG
2
Ligand/Ion
HEPTYL 1-THIOHEXOPYRANOSIDE
5
HTO
1
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
3
Ligand/Ion
PALMITIC ACID
9
RET
1
Ligand/Ion
RETINAL
10
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(37, 37)
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)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (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
ARG B:147 , PRO B:347 , BMA B:603
BINDING SITE FOR RESIDUE BMA B 602
05
AC5
SOFTWARE
LYS A:16 , ARG B:147 , BMA B:602 , NAG B:604
BINDING SITE FOR RESIDUE BMA B 603
06
AC6
SOFTWARE
LYS A:16 , ALA B:348 , 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
BINDING SITE FOR RESIDUE NAG A 704
09
AC9
SOFTWARE
ASN A:2 , GLY A:280 , SER A:281 , ASP A:282 , NAG A:704 , ZN B:956
BINDING SITE FOR RESIDUE NAG A 705
10
BC1
SOFTWARE
NAG B:805
BINDING SITE FOR RESIDUE NAG B 804
11
BC2
SOFTWARE
ASN B:2 , GLY B:280 , SER B:281 , ASP B:282 , NAG B:804
BINDING SITE FOR RESIDUE NAG B 805
12
BC3
SOFTWARE
CYS A:264 , THR A:297 , TYR A:301
BINDING SITE FOR RESIDUE HG A 901
13
BC4
SOFTWARE
ALA B:260 , CYS B:264 , THR B:297 , TYR B:301
BINDING SITE FOR RESIDUE HG B 902
14
BC5
SOFTWARE
CYS A:222 , TYR A:223
BINDING SITE FOR RESIDUE HG A 903
15
BC6
SOFTWARE
ALA B:132 , CYS B:222 , TYR B:223
BINDING SITE FOR RESIDUE HG B 904
16
BC7
SOFTWARE
GLN A:312 , CYS A:316 , VAL A:337
BINDING SITE FOR RESIDUE HG A 905
17
BC8
SOFTWARE
HIS B:65 , CYS B:316 , THR B:336 , VAL B:337 , SER B:338
BINDING SITE FOR RESIDUE HG B 906
18
BC9
SOFTWARE
NAG A:705 , HIS B:195 , GLU B:197
BINDING SITE FOR RESIDUE ZN B 956
19
CC1
SOFTWARE
GLU A:201 , GLN A:279 , GLU B:196
BINDING SITE FOR RESIDUE ZN A 957
20
CC2
SOFTWARE
GLU A:196 , GLU B:201 , GLN B:279
BINDING SITE FOR RESIDUE ZN B 958
21
CC3
SOFTWARE
LYS A:311 , GLY A:329 , ASP A:330 , HIS B:100
BINDING SITE FOR RESIDUE ZN A 959
22
CC4
SOFTWARE
GLU A:122 , TRP A:126 , MET A:163 , CYS A:167 , HIS A:211
BINDING SITE FOR RESIDUE ZN A 962
23
CC5
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
24
CC6
SOFTWARE
HIS A:195
BINDING SITE FOR RESIDUE ZN A 2011
25
CC7
SOFTWARE
ALA A:117 , GLU A:122 , CYS A:187 , TYR A:191 , PHE A:208 , HIS A:211 , PHE A:212 , TYR A:268 , LYS A:296 , HOH A:2014
BINDING SITE FOR RESIDUE RET A 1296
26
CC8
SOFTWARE
PRO A:53 , PHE A:56 , LEU A:57 , LEU A:321 , CYS A:322 , PLM A:1323 , MET B:49 , PHE B:52 , PHE B:88
BINDING SITE FOR RESIDUE PLM A 1322
27
CC9
SOFTWARE
LEU A:321 , CYS A:322 , CYS A:323 , PLM A:1322 , VAL B:81 , PHE B:85
BINDING SITE FOR RESIDUE PLM A 1323
28
DC1
SOFTWARE
GLU B:113 , ALA B:117 , GLU B:122 , MET B:207 , HIS B:211 , PHE B:212 , LYS B:296 , HOH B:2018
BINDING SITE FOR RESIDUE RET B 1296
29
DC2
SOFTWARE
PHE A:45 , LEU B:57 , CYS B:322 , PLM B:1323
BINDING SITE FOR RESIDUE PLM B 1322
30
DC3
SOFTWARE
PHE A:88 , LEU B:321 , CYS B:322 , CYS B:323 , PLM B:1322
BINDING SITE FOR RESIDUE PLM B 1323
31
DC4
SOFTWARE
MET B:308 , ARG B:314
BINDING SITE FOR RESIDUE HTO B 1401
32
DC5
SOFTWARE
LEU B:46 , TYR B:301
BINDING SITE FOR RESIDUE PLM B 1407
33
DC6
SOFTWARE
ILE A:259 , HTG A:1508
BINDING SITE FOR RESIDUE PLM A 1410
34
DC7
SOFTWARE
ASP B:282 , PHE B:283
BINDING SITE FOR RESIDUE HTG B 1506
35
DC8
SOFTWARE
LEU A:266 , PRO A:267 , VAL A:271 , PHE A:283 , PHE A:287
BINDING SITE FOR RESIDUE HTG A 1507
36
DC9
SOFTWARE
ARG A:252 , ILE A:256 , ILE A:305 , MET A:309 , PLM A:1410 , TRP B:35 , SER B:38 , ALA B:42
BINDING SITE FOR RESIDUE HTG A 1508
37
EC1
SOFTWARE
LEU A:99 , HIS A:100 , GLN A:344 , LYS B:311 , ARG B:314 , ASN B:315 , GLY B:329 , ASP B:330
BINDING SITE FOR RESIDUE HTG B 1509
[
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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, 4)
Info
All PROSITE Patterns/Profiles
1: G_PROTEIN_RECEP_F1_1 (A:123-139,B:123-139)
2: OPSIN (A:290-306,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
2
A:123-139
B:123-139
2
OPSIN
PS00238
Visual pigments (opsins) retinal binding site.
OPSD_BOVIN
290-306
2
A:290-306
B:290-306
[
close PROSITE info
]
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_d2hpya_ (A:)
1b: SCOP_d2hpyb_ (B:)
View:
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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
:
automated matches
(8)
Cow (Bos taurus) [TaxId: 9913]
(8)
1a
d2hpya_
A:
1b
d2hpyb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2hpyA00 (A:1-348)
1b: CATH_2hpyB00 (B:1-348)
View:
Select:
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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
2hpyA00
A:1-348
1b
2hpyB00
B: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
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