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1LNL
Biol. Unit 1
Info
Asym.Unit (184 KB)
Biol.Unit 1 (343 KB)
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(1)
Title
:
STRUCTURE OF DEOXYGENATED HEMOCYANIN FROM RAPANA THOMASIANA
Authors
:
M. Perbandt, E. W. Guthoehrlein, W. Rypniewski, K. Idakieva, S. Stoeva W. Voelter, N. Genov, C. Betzel
Date
:
03 May 02 (Deposition) - 03 Jun 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Hemocyanin, Deoxygenated Form, Oxygen, Metal Binding Site, Cooperativity, Oxygen Storage-Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Perbandt, E. W. Guthoehrlein, W. Rypniewski, K. Idakieva, S. Stoeva, W. Voelter, N. Genov, C. Betzel
The Structure Of A Functional Unit From The Wall Of A Gastropod Hemocyanin Offers A Possible Mechanism For Cooperativity
Biochemistry V. 42 6341 2003
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Hetero Components
(1, 6)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
1e: COPPER (II) ION (CUe)
1f: COPPER (II) ION (CUf)
1g: COPPER (II) ION (CUg)
1h: COPPER (II) ION (CUh)
1i: COPPER (II) ION (CUi)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CU
-1
Ligand/Ion
COPPER (II) ION
2
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:9 , LEU A:10 , SER A:11
BINDING SITE FOR RESIDUE NAG A 600
02
AC2
SOFTWARE
ASP C:112 , ASN C:119 , PHE C:120 , NAG C:651
BINDING SITE FOR RESIDUE NAG C 650
03
AC3
SOFTWARE
NAG C:650
BINDING SITE FOR RESIDUE NAG C 651
04
AC4
SOFTWARE
HIS A:41 , CYS A:59 , HIS A:61 , HIS A:70 , CU A:5012
BINDING SITE FOR RESIDUE CU A 5001
05
AC5
SOFTWARE
HIS A:70 , HIS A:181 , HIS A:185 , HIS A:212 , CU A:5001
BINDING SITE FOR RESIDUE CU A 5012
06
AC6
SOFTWARE
HIS A:-2 , ARG A:-1 , HIS B:117
BINDING SITE FOR RESIDUE CU B 5503
07
AC7
SOFTWARE
HIS B:41 , HIS B:61 , HIS B:70 , CU B:5015
BINDING SITE FOR RESIDUE CU B 5004
08
AC8
SOFTWARE
HIS B:70 , HIS B:181 , HIS B:185 , HIS B:212 , CU B:5004
BINDING SITE FOR RESIDUE CU B 5015
09
AC9
SOFTWARE
HIS B:-2 , ARG B:-1 , HIS C:277
BINDING SITE FOR RESIDUE CU B 5506
10
BC1
SOFTWARE
HIS C:41 , HIS C:61 , HIS C:70 , CU C:5018
BINDING SITE FOR RESIDUE CU C 5007
11
BC2
SOFTWARE
HIS C:70 , HIS C:181 , HIS C:185 , HIS C:212 , CU C:5007
BINDING SITE FOR RESIDUE CU C 5018
12
BC3
SOFTWARE
HIS B:277 , ARG C:-1 , HIS C:-2
BINDING SITE FOR RESIDUE CU C 5509
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: TYROSINASE_1 (A:61-78,B:61-78,C:61-78)
2: TYROSINASE_2 (A:205-216,B:205-216,C:205-216)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TYROSINASE_1
PS00497
Tyrosinase CuA-binding region signature.
HCY2E_RAPVE
69-86
6
A:61-78
B:61-78
C:61-78
2
TYROSINASE_2
PS00498
Tyrosinase and hemocyanins CuB-binding region signature.
HCY2E_RAPVE
213-224
6
A:205-216
B:205-216
C:205-216
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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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1lnla1 (A:-3-304)
1b: SCOP_d1lnlb1 (B:-3-304)
1c: SCOP_d1lnlc1 (C:-3-304)
2a: SCOP_d1lnla2 (A:305-405)
2b: SCOP_d1lnlb2 (B:305-405)
2c: SCOP_d1lnlc2 (C:305-405)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Di-copper centre-containing domain
(47)
Superfamily
:
Di-copper centre-containing domain
(47)
Family
:
Hemocyanin middle domain
(8)
Protein domain
:
Mollusc hemocyanin
(2)
Mollusca (Rapana thomasiana) [TaxId: 29165]
(1)
1a
d1lnla1
A:-3-304
1b
d1lnlb1
B:-3-304
1c
d1lnlc1
C:-3-304
Class
:
All beta proteins
(24004)
Fold
:
C-terminal domain of mollusc hemocyanin
(2)
Superfamily
:
C-terminal domain of mollusc hemocyanin
(2)
Family
:
C-terminal domain of mollusc hemocyanin
(2)
Protein domain
:
C-terminal domain of mollusc hemocyanin
(2)
Mollusca (Rapana thomasiana) [TaxId: 29165]
(1)
2a
d1lnla2
A:305-405
2b
d1lnlb2
B:305-405
2c
d1lnlc2
C:305-405
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1lnlA01 (A:-3-304)
1b: CATH_1lnlB01 (B:-3-304)
1c: CATH_1lnlC01 (C:-3-304)
2a: CATH_1lnlA02 (A:305-405)
2b: CATH_1lnlB02 (B:305-405)
2c: CATH_1lnlC02 (C:305-405)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
di-copper center containing domain from catechol oxidase
(13)
Homologous Superfamily
:
Di-copper center containing domain from catechol oxidase
(13)
Rapana thomasiana. Organism_taxid: 29165
(1)
1a
1lnlA01
A:-3-304
1b
1lnlB01
B:-3-304
1c
1lnlC01
C:-3-304
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Hemocyanin; Chain: A, domain 2
(2)
Homologous Superfamily
:
[code=2.60.310.10, no name defined]
(2)
Rapana thomasiana. Organism_taxid: 29165
(1)
2a
1lnlA02
A:305-405
2b
1lnlB02
B:305-405
2c
1lnlC02
C:305-405
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Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Tyrosinase_1lnlC01 (C:31-225)
1b: PFAM_Tyrosinase_1lnlC02 (C:31-225)
1c: PFAM_Tyrosinase_1lnlC03 (C:31-225)
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Organisms
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)
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)
Clan
:
Di-copper
(13)
Family
:
Tyrosinase
(10)
Rapana venosa (Veined rapa whelk) (Rapana thomasiana)
(1)
1a
Tyrosinase-1lnlC01
C:31-225
1b
Tyrosinase-1lnlC02
C:31-225
1c
Tyrosinase-1lnlC03
C:31-225
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Asymmetric Unit 1
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