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1KZU
Biol. Unit 1
Info
Asym.Unit (71 KB)
Biol.Unit 1 (174 KB)
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(1)
Title
:
INTEGRAL MEMBRANE PERIPHERAL LIGHT HARVESTING COMPLEX FROM RHODOPSEUDOMONAS ACIDOPHILA STRAIN 10050
Authors
:
R. J. Cogdell, A. A. Freer, N. W. Isaacs, A. M. Hawthornthwaite-Lawless G. Mcdermott, M. Z. Papiz, S. M. Prince
Date
:
31 Aug 96 (Deposition) - 01 Apr 97 (Release) - 30 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,D,E,G,H
Biol. Unit 1: A,B,D,E,G,H (3x)
Keywords
:
Antenna Complex, Light-Harvesting Protein, Lh2 Complex, Bacteriochlorophyll, Purple Bacteria
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. M. Prince, M. Z. Papiz, A. A. Freer, G. Mcdermott, A. M. Hawthornthwaite-Lawless, R. J. Cogdell, N. W. Isaacs
Apoprotein Structure In The Lh2 Complex From Rhodopseudomonas Acidophila Strain 10050: Modular Assembly And Protein Pigment Interactions.
J. Mol. Biol. V. 268 412 1997
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 54)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
1d: BACTERIOCHLOROPHYLL A (BCLd)
1e: BACTERIOCHLOROPHYLL A (BCLe)
1f: BACTERIOCHLOROPHYLL A (BCLf)
1g: BACTERIOCHLOROPHYLL A (BCLg)
1h: BACTERIOCHLOROPHYLL A (BCLh)
1i: BACTERIOCHLOROPHYLL A (BCLi)
2a: N-FORMYLMETHIONINE (FMEa)
2b: N-FORMYLMETHIONINE (FMEb)
2c: N-FORMYLMETHIONINE (FMEc)
3a: RHODOPIN B-D-GLUCOSIDE (RG1a)
3b: RHODOPIN B-D-GLUCOSIDE (RG1b)
3c: RHODOPIN B-D-GLUCOSIDE (RG1c)
3d: RHODOPIN B-D-GLUCOSIDE (RG1d)
3e: RHODOPIN B-D-GLUCOSIDE (RG1e)
3f: RHODOPIN B-D-GLUCOSIDE (RG1f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
27
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
FME
9
Mod. Amino Acid
N-FORMYLMETHIONINE
3
RG1
18
Ligand/Ion
RHODOPIN B-D-GLUCOSIDE
[
close Hetero Component info
]
Sites
(24, 24)
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: BB (UNKNOWN)
11: BBA (UNKNOWN)
12: BBB (UNKNOWN)
13: BC1 (SOFTWARE)
14: BC2 (SOFTWARE)
15: BC3 (SOFTWARE)
16: BC4 (SOFTWARE)
17: BC5 (SOFTWARE)
18: BC6 (SOFTWARE)
19: EE (UNKNOWN)
20: EEA (UNKNOWN)
21: EEB (UNKNOWN)
22: HH (UNKNOWN)
23: HHA (UNKNOWN)
24: HHB (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:23 , ILE A:26 , BCL A:56 , LEU B:3 , GLN B:7 , LEU B:11 , TYR B:14 , GLY B:18 , THR B:19 , BCL B:43 , TRP D:45 , BCL D:55 , GLN G:3 , THR G:8 , BCL G:56 , BCL H:43
BINDING SITE FOR RESIDUE RG1 B 42
02
AC2
SOFTWARE
TYR A:44 , BCL A:55 , ALA B:29 , LEU B:32 , ALA B:36 , BCL H:43
BINDING SITE FOR RESIDUE RG1 A 54
03
AC3
SOFTWARE
GLN A:3 , THR A:8 , BCL A:56 , BCL B:43 , VAL D:23 , ILE D:26 , BCL D:56 , LEU E:3 , GLN E:7 , LEU E:11 , TYR E:14 , GLY E:18 , THR E:19 , BCL E:43 , TRP G:45 , BCL G:55
BINDING SITE FOR RESIDUE RG1 E 42
04
AC4
SOFTWARE
BCL B:43 , TYR D:44 , BCL D:55 , ALA E:29 , LEU E:32 , ALA E:36
BINDING SITE FOR RESIDUE RG1 D 54
05
AC5
SOFTWARE
TRP A:45 , BCL A:55 , GLN D:3 , THR D:8 , BCL D:56 , BCL E:43 , VAL G:23 , ILE G:26 , BCL G:56 , LEU H:3 , GLN H:7 , LEU H:11 , TYR H:14 , GLY H:18 , THR H:19 , BCL H:43
BINDING SITE FOR RESIDUE RG1 H 42
06
AC6
SOFTWARE
BCL E:43 , TYR G:44 , BCL G:55 , ALA H:29 , LEU H:32 , ALA H:36
BINDING SITE FOR RESIDUE RG1 G 54
07
AC7
SOFTWARE
THR A:24 , ALA A:27 , HIS A:31 , TRP A:45 , RG1 A:54 , PHE B:22 , LEU B:25 , ALA B:26 , ALA B:29 , HIS B:30 , BCL B:43 , VAL G:10 , BCL G:56 , RG1 H:42 , BCL H:43
BINDING SITE FOR RESIDUE BCL A 55
08
AC8
SOFTWARE
VAL A:23 , ALA A:27 , VAL A:30 , HIS A:31 , ILE A:34 , BCL A:55 , BCL A:56 , THR B:19 , PHE B:22 , ALA B:26 , HIS B:30 , TRP B:39 , RG1 B:42 , TYR D:44 , TRP D:45 , RG1 D:54 , BCL D:55 , PHE E:22 , RG1 E:42
BINDING SITE FOR RESIDUE BCL B 43
09
AC9
SOFTWARE
FME A:1 , ASN A:2 , HOH A:57 , ILE B:16 , THR B:19 , ARG B:20 , HIS B:30 , TRP B:39 , RG1 B:42 , BCL B:43 , BCL D:55 , GLY E:18 , RG1 E:42
BINDING SITE FOR RESIDUE BCL A 56
10
BB
UNKNOWN
FME A:1 , ARG B:20
B800 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
11
BBA
UNKNOWN
HIS A:31 , TRP A:45
B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
12
BBB
UNKNOWN
HIS B:30 , TYR A:44
B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
13
BC1
SOFTWARE
VAL A:10 , BCL A:56 , RG1 B:42 , BCL B:43 , THR D:24 , ALA D:27 , HIS D:31 , TRP D:45 , RG1 D:54 , PHE E:22 , LEU E:25 , ALA E:26 , ALA E:29 , HIS E:30 , BCL E:43
BINDING SITE FOR RESIDUE BCL D 55
14
BC2
SOFTWARE
VAL D:23 , ALA D:27 , VAL D:30 , HIS D:31 , ILE D:34 , BCL D:55 , BCL D:56 , THR E:19 , PHE E:22 , ALA E:26 , HIS E:30 , TRP E:39 , RG1 E:42 , TYR G:44 , TRP G:45 , RG1 G:54 , BCL G:55 , PHE H:22 , RG1 H:42
BINDING SITE FOR RESIDUE BCL E 43
15
BC3
SOFTWARE
FME D:1 , ASN D:2 , HOH D:57 , ILE E:16 , THR E:19 , ARG E:20 , HIS E:30 , TRP E:39 , RG1 E:42 , BCL E:43 , BCL G:55 , GLY H:18 , RG1 H:42
BINDING SITE FOR RESIDUE BCL D 56
16
BC4
SOFTWARE
VAL D:10 , BCL D:56 , RG1 E:42 , BCL E:43 , THR G:24 , ALA G:27 , HIS G:31 , TRP G:45 , RG1 G:54 , PHE H:22 , LEU H:25 , ALA H:26 , ALA H:29 , HIS H:30 , BCL H:43
BINDING SITE FOR RESIDUE BCL G 55
17
BC5
SOFTWARE
TYR A:44 , TRP A:45 , RG1 A:54 , BCL A:55 , PHE B:22 , RG1 B:42 , VAL G:23 , ALA G:27 , VAL G:30 , HIS G:31 , ILE G:34 , BCL G:55 , BCL G:56 , THR H:19 , PHE H:22 , ALA H:26 , HIS H:30 , TRP H:39 , RG1 H:42
BINDING SITE FOR RESIDUE BCL H 43
18
BC6
SOFTWARE
BCL A:55 , GLY B:18 , RG1 B:42 , FME G:1 , ASN G:2 , HOH G:57 , ILE H:16 , THR H:19 , ARG H:20 , HIS H:30 , TRP H:39 , RG1 H:42 , BCL H:43
BINDING SITE FOR RESIDUE BCL G 56
19
EE
UNKNOWN
FME D:1 , ARG E:20
B800 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
20
EEA
UNKNOWN
HIS D:31 , TRP D:45
B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
21
EEB
UNKNOWN
HIS E:30 , TYR D:44
B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
22
HH
UNKNOWN
FME G:1 , ARG H:20
B800 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
23
HHA
UNKNOWN
HIS G:31 , TRP G:45
B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
24
HHB
UNKNOWN
HIS H:30 , TYR G:44
B850 BACTERIOCHLOROPHYLL COORDINATING RESIDUES.
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 18)
Info
All PROSITE Patterns/Profiles
1: ANTENNA_COMP_BETA (B:7-38,E:7-38,H:7-38)
2: ANTENNA_COMP_ALPHA (A:25-41,D:25-41,G:25-41)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ANTENNA_COMP_BETA
PS00969
Antenna complexes beta subunits signature.
LHB5_RHOAC
7-38
9
B:7-38
E:7-38
H:7-38
2
ANTENNA_COMP_ALPHA
PS00968
Antenna complexes alpha subunits signature.
LHA4_RHOAC
25-41
9
A:25-41
D:25-41
G:25-41
[
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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, 6)
Info
All SCOP Domains
1a: SCOP_d1kzua_ (A:)
1b: SCOP_d1kzub_ (B:)
1c: SCOP_d1kzud_ (D:)
1d: SCOP_d1kzue_ (E:)
1e: SCOP_d1kzug_ (G:)
1f: SCOP_d1kzuh_ (H:)
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Classes
(
)
(
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Folds
(
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(
)
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Light-harvesting complex subunits
(9)
Superfamily
:
Light-harvesting complex subunits
(9)
Family
:
Light-harvesting complex subunits
(8)
Protein domain
:
Light-harvesting complex subunits
(8)
Rhodoblastus acidophilus [TaxId: 1074]
(4)
1a
d1kzua_
A:
1b
d1kzub_
B:
1c
d1kzud_
D:
1d
d1kzue_
E:
1e
d1kzug_
G:
1f
d1kzuh_
H:
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1kzuA00 (A:2-49)
1b: CATH_1kzuD00 (D:2-49)
1c: CATH_1kzuG00 (G:2-49)
2a: CATH_1kzuB00 (B:1-41)
2b: CATH_1kzuE00 (E:1-41)
2c: CATH_1kzuH00 (H:1-41)
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Classes
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Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Light-harvesting Protein
(6)
Homologous Superfamily
:
[code=4.10.220.20, no name defined]
(5)
Rhodoblastus acidophilus. Organism_taxid: 1074. Strain: 10050.
(2)
1a
1kzuA00
A:2-49
1b
1kzuD00
D:2-49
1c
1kzuG00
G:2-49
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.250, no name defined]
(9)
Rhodoblastus acidophilus. Organism_taxid: 1074. Strain: 10050.
(2)
2a
1kzuB00
B:1-41
2b
1kzuE00
E:1-41
2c
1kzuH00
H:1-41
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_LHC_1kzuG01 (G:3-42)
1b: PFAM_LHC_1kzuG02 (G:3-42)
1c: PFAM_LHC_1kzuG03 (G:3-42)
1d: PFAM_LHC_1kzuH01 (H:5-41)
1e: PFAM_LHC_1kzuH02 (H:5-41)
1f: PFAM_LHC_1kzuH03 (H:5-41)
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Clans
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(
)
Organisms
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)
(
)
Clan
:
no clan defined [family: LHC]
(5)
Family
:
LHC
(5)
Rhodopseudomonas acidophila (Rhodoblastus acidophilus)
(2)
1a
LHC-1kzuG01
G:3-42
1b
LHC-1kzuG02
G:3-42
1c
LHC-1kzuG03
G:3-42
1d
LHC-1kzuH01
H:5-41
1e
LHC-1kzuH02
H:5-41
1f
LHC-1kzuH03
H:5-41
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