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1NKZ
Asym. Unit
Info
Asym.Unit (92 KB)
Biol.Unit 1 (208 KB)
Biol.Unit 2 (411 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LH2 B800-850 FROM RPS. ACIDOPHILA AT 2.0 ANGSTROM RESOLUTION
Authors
:
M. Z. Papiz, S. M. Prince, T. Howard, R. J. Cogdell, N. W. Isaacs
Date
:
06 Jan 03 (Deposition) - 25 Feb 03 (Release) - 01 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (3x)
Biol. Unit 2: A,B,C,D,E,F (6x)
Keywords
:
Light Harvesting Complex Ii, Trans-Membrane Helices, Rhodopin Glucoside, Bacteriochlorophyll A, Photosynthesis, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Z. Papiz, S. M. Prince, T. Howard, R. J. Cogdell, N. W. Isaacs
The Structure And Thermal Motion Of The B800-850 Lh2 Comple From Rps. Acidophila At 2. 0 A Resolution And 100K : New Structural Features And Functionally Relevant Motions.
J. Mol. Biol. V. 326 1523 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 27)
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: BENZAMIDINE (BENa)
2b: BENZAMIDINE (BENb)
2c: BENZAMIDINE (BENc)
3a: B-OCTYLGLUCOSIDE (BOGa)
3b: B-OCTYLGLUCOSIDE (BOGb)
3c: B-OCTYLGLUCOSIDE (BOGc)
3d: B-OCTYLGLUCOSIDE (BOGd)
3e: B-OCTYLGLUCOSIDE (BOGe)
3f: B-OCTYLGLUCOSIDE (BOGf)
4a: N-CARBOXYMETHIONINE (CXMa)
4b: N-CARBOXYMETHIONINE (CXMb)
4c: N-CARBOXYMETHIONINE (CXMc)
5a: RHODOPIN B-D-GLUCOSIDE (RG1a)
5b: RHODOPIN B-D-GLUCOSIDE (RG1b)
5c: RHODOPIN B-D-GLUCOSIDE (RG1c)
5d: RHODOPIN B-D-GLUCOSIDE (RG1d)
5e: RHODOPIN B-D-GLUCOSIDE (RG1e)
5f: RHODOPIN B-D-GLUCOSIDE (RG1f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
9
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BEN
3
Ligand/Ion
BENZAMIDINE
3
BOG
6
Ligand/Ion
B-OCTYLGLUCOSIDE
4
CXM
3
Mod. Amino Acid
N-CARBOXYMETHIONINE
5
RG1
6
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: 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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:23 , BCL A:307 , GLU B:10 , TYR B:14 , GLY B:18 , THR B:19 , BCL B:302 , HOH B:436 , TRP C:45 , BCL C:303 , GLN E:3 , LYS E:5 , ILE E:6 , BCL E:309 , ALA F:5 , BCL F:306
BINDING SITE FOR RESIDUE RG1 B 401
02
AC2
SOFTWARE
GLN A:3 , LYS A:5 , BCL A:307 , BCL B:302 , VAL C:23 , BCL C:308 , GLU D:10 , TYR D:14 , GLY D:18 , THR D:19 , BCL D:304 , HOH D:408 , HOH D:426 , HOH D:436 , HOH D:440 , TRP E:45 , BCL E:305
BINDING SITE FOR RESIDUE RG1 D 402
03
AC3
SOFTWARE
HIS A:31 , BCL A:301 , GLN C:3 , LYS C:5 , BCL C:308 , BCL D:304 , VAL E:23 , BCL E:309 , GLU F:10 , TYR F:14 , GLY F:18 , THR F:19 , BCL F:306 , HOH F:310
BINDING SITE FOR RESIDUE RG1 C 403
04
AC4
SOFTWARE
TRP A:40 , ALA A:43 , TYR A:44 , VAL A:49 , BCL A:301 , HOH A:516 , HOH A:535 , ALA B:29 , ALA B:36 , THR B:37 , VAL C:49 , LYS C:51 , ALA C:52 , RG1 C:405 , HOH C:522 , HIS F:41 , BCL F:306
BINDING SITE FOR RESIDUE RG1 A 404
05
AC5
SOFTWARE
VAL A:49 , LYS A:51 , ALA A:52 , RG1 A:404 , HOH A:516 , HOH A:525 , HIS B:41 , BCL B:302 , TRP C:40 , ALA C:43 , TYR C:44 , VAL C:49 , BCL C:303 , HOH C:522 , HOH C:539 , HOH C:549 , ALA D:29 , ALA D:36 , THR D:37 , HOH D:420
BINDING SITE FOR RESIDUE RG1 C 405
06
AC6
SOFTWARE
HIS D:41 , TRP E:40 , ALA E:43 , TYR E:44 , GLY E:47 , VAL E:49 , LYS E:51 , ALA E:52 , BCL E:305 , HOH E:519 , HOH E:525 , HOH E:542 , HOH E:546 , HOH E:548 , ALA F:29 , ALA F:36 , THR F:37 , PRO F:38
BINDING SITE FOR RESIDUE RG1 E 406
07
AC7
SOFTWARE
ILE C:14 , ALA C:18 , SER C:22 , VAL C:25 , BEN C:510 , HOH C:531 , HOH C:541 , BEN E:511
BINDING SITE FOR RESIDUE BOG C 504
08
AC8
SOFTWARE
ILE E:14 , ALA E:18 , SER E:22 , VAL E:25 , BEN E:511 , BEN E:512 , HOH E:536 , HOH E:551
BINDING SITE FOR RESIDUE BOG E 505
09
AC9
SOFTWARE
ILE A:14 , ALA A:18 , VAL A:25 , BEN C:510 , BEN E:512 , HOH E:556 , HOH E:559
BINDING SITE FOR RESIDUE BOG E 506
10
BC1
SOFTWARE
ALA A:33 , HIS A:37 , LEU C:32 , LEU C:35 , BOG C:508 , HOH C:530
BINDING SITE FOR RESIDUE BOG A 507
11
BC2
SOFTWARE
BOG A:507 , SER C:36 , HIS C:37 , HOH C:525 , LEU E:32 , HOH E:557
BINDING SITE FOR RESIDUE BOG C 508
12
BC3
SOFTWARE
LEU A:32 , HOH A:527 , SER E:36 , HIS E:37 , HOH E:535 , HOH E:547 , HOH E:557
BINDING SITE FOR RESIDUE BOG E 509
13
BC4
SOFTWARE
LEU A:20 , THR A:24 , ALA A:27 , HIS A:31 , TRP A:40 , PHE A:41 , TRP A:45 , RG1 A:404 , HOH A:526 , PHE B:22 , ALA B:26 , ALA B:29 , HIS B:30 , BCL B:302 , RG1 C:403 , GLY E:15 , SER E:22 , BCL E:309 , BCL F:306
BINDING SITE FOR RESIDUE BCL A 301
14
BC5
SOFTWARE
VAL A:23 , ILE A:26 , ALA A:27 , VAL A:30 , HIS A:31 , ILE A:34 , BCL A:301 , BCL A:307 , THR B:19 , PHE B:22 , LEU B:23 , ALA B:26 , HIS B:30 , TRP B:39 , RG1 B:401 , TYR C:44 , TRP C:45 , BCL C:303 , RG1 C:405 , RG1 D:402
BINDING SITE FOR RESIDUE BCL B 302
15
BC6
SOFTWARE
GLY A:15 , SER A:22 , BCL A:307 , BCL B:302 , RG1 B:401 , LEU C:20 , THR C:24 , ALA C:27 , HIS C:31 , TRP C:40 , PHE C:41 , TRP C:45 , RG1 C:405 , PHE D:22 , ALA D:26 , ALA D:29 , HIS D:30 , BCL D:304 , HOH D:420
BINDING SITE FOR RESIDUE BCL C 303
16
BC7
SOFTWARE
VAL C:23 , ALA C:27 , VAL C:30 , HIS C:31 , ILE C:34 , BCL C:303 , BCL C:308 , RG1 C:403 , THR D:19 , PHE D:22 , LEU D:23 , ALA D:26 , HIS D:30 , TRP D:39 , RG1 D:402 , TYR E:44 , TRP E:45 , BCL E:305
BINDING SITE FOR RESIDUE BCL D 304
17
BC8
SOFTWARE
GLY C:15 , SER C:22 , BCL C:308 , BCL D:304 , RG1 D:402 , LEU E:20 , THR E:24 , ALA E:27 , HIS E:31 , PHE E:41 , TRP E:45 , RG1 E:406 , BEN E:511 , PHE F:22 , ALA F:26 , ALA F:29 , HIS F:30 , BCL F:306
BINDING SITE FOR RESIDUE BCL E 305
18
BC9
SOFTWARE
TYR A:44 , TRP A:45 , BCL A:301 , RG1 A:404 , RG1 B:401 , RG1 C:403 , VAL E:23 , ALA E:27 , VAL E:30 , HIS E:31 , ILE E:34 , BCL E:305 , BCL E:309 , THR F:19 , PHE F:22 , LEU F:23 , ALA F:26 , HIS F:30 , TRP F:39
BINDING SITE FOR RESIDUE BCL F 306
19
CC1
SOFTWARE
CXM A:1 , ASN A:2 , GLN A:3 , ALA A:53 , HOH A:508 , ILE B:16 , THR B:19 , ARG B:20 , HIS B:30 , BCL B:302 , RG1 B:401 , BCL C:303 , GLY D:18 , RG1 D:402
BINDING SITE FOR RESIDUE BCL A 307
20
CC2
SOFTWARE
CXM C:1 , ASN C:2 , GLN C:3 , RG1 C:403 , HOH C:511 , ILE D:16 , THR D:19 , ARG D:20 , BCL D:304 , RG1 D:402 , ALA E:53 , BCL E:305 , GLY F:18
BINDING SITE FOR RESIDUE BCL C 308
21
CC3
SOFTWARE
BCL A:301 , GLY B:18 , RG1 B:401 , ALA C:53 , RG1 C:403 , HOH C:553 , CXM E:1 , ASN E:2 , GLN E:3 , HOH E:513 , ILE F:16 , THR F:19 , ARG F:20 , BCL F:306
BINDING SITE FOR RESIDUE BCL E 309
22
CC4
SOFTWARE
SER A:22 , VAL A:25 , GLY C:21 , THR C:24 , BOG C:504 , BOG E:506
BINDING SITE FOR RESIDUE BEN C 510
23
CC5
SOFTWARE
SER C:22 , BOG C:504 , THR E:24 , BCL E:305 , BOG E:505
BINDING SITE FOR RESIDUE BEN E 511
24
CC6
SOFTWARE
GLY A:21 , THR A:24 , ILE A:28 , SER E:22 , BOG E:505 , BOG E:506
BINDING SITE FOR RESIDUE BEN E 512
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: ANTENNA_COMP_BETA (B:7-38,D:7-38,F:7-38)
2: ANTENNA_COMP_ALPHA (A:25-41,C:25-41,E:25-41)
;
View:
Select:
Label:
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
3
B:7-38
D:7-38
F:7-38
2
ANTENNA_COMP_ALPHA
PS00968
Antenna complexes alpha subunits signature.
LHA4_RHOAC
25-41
3
A:25-41
C:25-41
E:25-41
[
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1nkza_ (A:)
1b: SCOP_d1nkzb_ (B:)
1c: SCOP_d1nkzc_ (C:)
1d: SCOP_d1nkzd_ (D:)
1e: SCOP_d1nkze_ (E:)
1f: SCOP_d1nkzf_ (F:)
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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
d1nkza_
A:
1b
d1nkzb_
B:
1c
d1nkzc_
C:
1d
d1nkzd_
D:
1e
d1nkze_
E:
1f
d1nkzf_
F:
[
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]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1nkzA00 (A:2-53)
1b: CATH_1nkzC00 (C:2-53)
1c: CATH_1nkzE00 (E:2-53)
2a: CATH_1nkzB00 (B:1-41)
2b: CATH_1nkzD00 (D:1-41)
2c: CATH_1nkzF00 (F:1-41)
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Topologies
(
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(
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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.
(1)
1a
1nkzA00
A:2-53
1b
1nkzC00
C:2-53
1c
1nkzE00
E:2-53
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.
(1)
2a
1nkzB00
B:1-41
2b
1nkzD00
D:1-41
2c
1nkzF00
F:1-41
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_LHC_1nkzE01 (E:3-42)
1b: PFAM_LHC_1nkzE02 (E:3-42)
1c: PFAM_LHC_1nkzE03 (E:3-42)
1d: PFAM_LHC_1nkzF01 (F:5-41)
1e: PFAM_LHC_1nkzF02 (F:5-41)
1f: PFAM_LHC_1nkzF03 (F:5-41)
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Clans
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(
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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-1nkzE01
E:3-42
1b
LHC-1nkzE02
E:3-42
1c
LHC-1nkzE03
E:3-42
1d
LHC-1nkzF01
F:5-41
1e
LHC-1nkzF02
F:5-41
1f
LHC-1nkzF03
F:5-41
[
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