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2QPD
Asym. Unit
Info
Asym.Unit (133 KB)
Biol.Unit 1 (125 KB)
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(1)
Title
:
AN UNEXPECTED OUTCOME OF SURFACE-ENGINEERING AN INTEGRAL MEMBRANE PROTEIN: IMPROVED CRYSTALLIZATION OF CYTOCHROME BA3 OXIDASE FROM THERMUS THERMOPHILUS
Authors
:
B. Liu, V. M. Luna, Y. Chen, C. D. Stout, J. A. Fee
Date
:
23 Jul 07 (Deposition) - 11 Dec 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.25
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Cytochrome Ba3 Oxidase, Heme, Integral Membrane Protein, Electron Transport, Hydrogen Ion Transport, Ion Transport, Iron, Metal- Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport, Formylation
(Keyword Search:
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Reference
:
B. Liu, V. M. Luna, Y. Chen, C. D. Stout, J. A. Fee
An Unexpected Outcome Of Surface Engineering An Integral Membrane Protein: Improved Crystallization Of Cytochrome Ba(3) From Thermus Thermophilus.
Acta Crystallogr. , Sect. F V. 63 1029 2007
(for further references see the
PDB file header
)
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Hetero Components
(4, 4)
Info
All Hetero Components
1a: COPPER (I) ION (CU1a)
2a: DINUCLEAR COPPER ION (CUAa)
3a: HEME-AS (HASa)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU1
1
Ligand/Ion
COPPER (I) ION
2
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
3
HAS
1
Ligand/Ion
HEME-AS
4
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:233 , HIS A:282 , HIS A:283
BINDING SITE FOR RESIDUE CU1 A 803
2
AC2
SOFTWARE
GLY A:39 , GLN A:42 , TYR A:46 , TYR A:65 , LEU A:69 , HIS A:72 , ASN A:76 , ALA A:77 , TYR A:133 , PHE A:385 , HIS A:386 , VAL A:389 , ALA A:390 , MET A:435 , ARG A:449 , ARG A:450 , ALA A:451
BINDING SITE FOR RESIDUE HEM A 800
3
AC3
SOFTWARE
TYR A:133 , VAL A:236 , TYR A:237 , TRP A:239 , TYR A:244 , HIS A:282 , HIS A:283 , THR A:302 , SER A:309 , ALA A:313 , ALA A:317 , VAL A:350 , LEU A:353 , LEU A:354 , PHE A:356 , ILE A:357 , GLY A:360 , GLY A:363 , ASN A:366 , ASP A:372 , HIS A:376 , VAL A:381 , HIS A:384 , PHE A:385 , GLN A:388 , VAL A:389 , ARG A:449
BINDING SITE FOR RESIDUE HAS A 801
4
AC4
SOFTWARE
HIS B:114 , CYS B:149 , GLN B:151 , CYS B:153 , HIS B:157 , MET B:160
BINDING SITE FOR RESIDUE CUA B 802
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: COX1 (A:7-560)
2: COX2_CUA (B:66-168)
3: COX2 (B:112-160)
4: COX1_CUB (A:229-283)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX1
PS50855
Cytochrome oxidase subunit I profile.
COX1_THET8
7-560
1
A:7-560
2
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_THET8
66-168
1
B:66-168
3
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_THET8
112-160
1
B:112-160
4
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1_THET8
229-283
1
A:229-283
[
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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.
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2qpdb1 (B:37-168)
2a: SCOP_d2qpdc1 (C:2-34)
3a: SCOP_d2qpdb2 (B:3-36)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Periplasmic domain of cytochrome c oxidase subunit II
(70)
Protein domain
:
Cytochrome c oxidase
(62)
Thermus thermophilus, ba3 type [TaxId: 274]
(28)
1a
d2qpdb1
B:37-168
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Bacterial ba3 type cytochrome c oxidase subunit IIa
(23)
Family
:
Bacterial ba3 type cytochrome c oxidase subunit IIa
(23)
Protein domain
:
Bacterial ba3 type cytochrome c oxidase subunit IIa
(23)
Thermus thermophilus [TaxId: 274]
(23)
2a
d2qpdc1
C:2-34
Fold
:
Transmembrane helix hairpin
(84)
Superfamily
:
Cytochrome c oxidase subunit II-like, transmembrane region
(66)
Family
:
Cytochrome c oxidase subunit II-like, transmembrane region
(57)
Protein domain
:
Bacterial ba3 type cytochrome c oxidase subunit II
(18)
Thermus thermophilus [TaxId: 274]
(18)
3a
d2qpdb2
B:3-36
[
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]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2qpdA00 (A:6-562)
2a: CATH_2qpdB01 (B:3-46)
3a: CATH_2qpdB02 (B:47-168)
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Classes
(
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome C Oxidase; Chain A
(41)
Homologous Superfamily
:
Cytochrome C Oxidase, chain A
(41)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(5)
1a
2qpdA00
A:6-562
Topology
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Homologous Superfamily
:
Rhopdopsin 7-helix transmembrane proteins
(128)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(5)
2a
2qpdB01
B:3-46
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(5)
3a
2qpdB02
B:47-168
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Pfam Domains
(4, 4)
Info
all PFAM domains
1a: PFAM_COX2_2qpdB01 (B:83-167)
2a: PFAM_COX1_2qpdA01 (A:17-483)
3a: PFAM_COX2_transmemb_2qpdB02 (B:3-40)
4a: PFAM_CoxIIa_2qpdC01 (C:2-34)
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Clans
(
)
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)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
COX2
(19)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
1a
COX2-2qpdB01
B:83-167
Clan
:
no clan defined [family: COX1]
(19)
Family
:
COX1
(19)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
2a
COX1-2qpdA01
A:17-483
Clan
:
no clan defined [family: COX2-transmemb]
(2)
Family
:
COX2-transmemb
(2)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
3a
COX2-transmemb-2qpdB02
B:3-40
Clan
:
no clan defined [family: CoxIIa]
(2)
Family
:
CoxIIa
(2)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
4a
CoxIIa-2qpdC01
C:2-34
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Asymmetric Unit 1
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