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1V0F
Asym. Unit
Info
Asym.Unit (645 KB)
Biol.Unit 1 (324 KB)
Biol.Unit 2 (325 KB)
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(1)
Title
:
ENDOSIALIDASE OF BACTERIOPHAGE K1F IN COMPLEX WITH OLIGOMERIC ALPHA-2,8-SIALIC ACID
Authors
:
K. Stummeyer, A. Dickmanns, M. Muehlenhoff, R. Gerady-Schahn, R. Ficner
Date
:
28 Mar 04 (Deposition) - 13 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Endosialidase, Polysialic Acid Degradation, Hydrolase, Glycosidase.
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Stummeyer, A. Dickmanns, M. Muehlenhoff, R. Gerardy-Schahn, R. Ficner
Crystal Structure Of The Polysialic Acid-Degrading Endosialidase Of Bacteriophage K1F
Nat. Struct. Mol. Biol. V. 12 90 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 18)
Info
All Hetero Components
1a: PHOSPHATE ION (PO4a)
1b: PHOSPHATE ION (PO4b)
1c: PHOSPHATE ION (PO4c)
1d: PHOSPHATE ION (PO4d)
1e: PHOSPHATE ION (PO4e)
1f: PHOSPHATE ION (PO4f)
2a: O-SIALIC ACID (SIAa)
2b: O-SIALIC ACID (SIAb)
2c: O-SIALIC ACID (SIAc)
2d: O-SIALIC ACID (SIAd)
2e: O-SIALIC ACID (SIAe)
2f: O-SIALIC ACID (SIAf)
3a: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBa)
3b: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBb)
3c: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBc)
3d: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBd)
3e: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBe)
3f: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PO4
6
Ligand/Ion
PHOSPHATE ION
2
SIA
6
Ligand/Ion
O-SIALIC ACID
3
SLB
6
Ligand/Ion
5-N-ACETYL-BETA-D-NEURAMINIC ACID
[
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]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:837 , THR A:846 , SER A:848 , GLN A:853 , HOH A:2175 , TYR B:821
BINDING SITE FOR RESIDUE SLB A1685
02
AC2
SOFTWARE
ARG B:837 , ILE B:839 , THR B:846 , SER B:848 , GLN B:853 , HOH B:2178
BINDING SITE FOR RESIDUE SLB B1685
03
AC3
SOFTWARE
TYR A:821 , ARG C:837 , ILE C:839 , THR C:846 , SER C:848 , GLN C:853 , ASN C:870 , HOH C:2127
BINDING SITE FOR RESIDUE SLB C1685
04
AC4
SOFTWARE
SER C:462 , VAL C:464 , GLY C:466 , VAL C:467 , SER C:468 , SIA C:1688
BINDING SITE FOR RESIDUE SIA C1686
05
AC5
SOFTWARE
THR B:728 , PHE C:459 , SER C:460 , ASN C:461 , SER C:468 , SIA C:1686 , HOH C:2129 , HOH C:2130
BINDING SITE FOR RESIDUE SIA C1688
06
AC6
SOFTWARE
ARG D:837 , ILE D:839 , THR D:846 , SER D:848 , GLN D:853 , HOH D:2148 , HOH D:2150 , TYR F:821
BINDING SITE FOR RESIDUE SLB D1685
07
AC7
SOFTWARE
VAL D:464 , THR D:465 , GLY D:466 , SER D:468 , SIA D:1688
BINDING SITE FOR RESIDUE SIA D1686
08
AC8
SOFTWARE
PHE D:459 , SER D:460 , ASN D:461 , SER D:468 , SIA D:1686 , HOH D:2048 , HOH D:2167 , THR E:728 , SER E:733
BINDING SITE FOR RESIDUE SIA D1688
09
AC9
SOFTWARE
TYR D:821 , ARG E:837 , ILE E:839 , THR E:846 , SER E:848 , GLN E:853 , HOH E:2127
BINDING SITE FOR RESIDUE SLB E1685
10
BC1
SOFTWARE
SER E:462 , VAL E:464 , GLY E:466 , SER E:468 , SIA E:1688 , HOH E:2129
BINDING SITE FOR RESIDUE SIA E1686
11
BC2
SOFTWARE
PHE E:459 , SER E:460 , ASN E:461 , SER E:468 , SIA E:1686 , HOH E:2130 , THR F:728 , TYR F:729
BINDING SITE FOR RESIDUE SIA E1688
12
BC3
SOFTWARE
ARG F:837 , THR F:846 , SER F:848 , GLN F:853 , HOH F:2140
BINDING SITE FOR RESIDUE SLB F1685
13
BC4
SOFTWARE
GLU A:818 , GLY A:819 , HOH A:2176 , PRO C:829 , THR C:830
BINDING SITE FOR RESIDUE PO4 A1686
14
BC5
SOFTWARE
PRO A:829 , THR A:830 , GLU B:818 , GLY B:819
BINDING SITE FOR RESIDUE PO4 B1686
15
BC6
SOFTWARE
ALA A:805 , PRO B:829 , THR B:830 , GLU C:818 , GLY C:819 , HOH C:2128
BINDING SITE FOR RESIDUE PO4 C1687
16
BC7
SOFTWARE
GLU D:818 , GLY D:819 , HOH D:2146 , PRO E:829 , THR E:830 , ALA F:805
BINDING SITE FOR RESIDUE PO4 D1687
17
BC8
SOFTWARE
ALA D:805 , GLU E:818 , GLY E:819 , THR F:830
BINDING SITE FOR RESIDUE PO4 F1686
18
BC9
SOFTWARE
PRO D:829 , THR D:830 , GLU F:818 , GLY F:819
BINDING SITE FOR RESIDUE PO4 F1687
[
close Site info
]
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
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1v0fa1 (A:245-760)
1b: SCOP_d1v0fe1 (E:245-760)
1c: SCOP_d1v0ff1 (F:245-760)
1d: SCOP_d1v0fb1 (B:245-760)
1e: SCOP_d1v0fc1 (C:245-760)
1f: SCOP_d1v0fd1 (D:245-760)
2a: SCOP_d1v0fa2 (A:761-910)
2b: SCOP_d1v0fe2 (E:761-910)
2c: SCOP_d1v0ff2 (F:761-910)
2d: SCOP_d1v0fb2 (B:761-910)
2e: SCOP_d1v0fc2 (C:761-910)
2f: SCOP_d1v0fd2 (D:761-910)
View:
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Classes
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)
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)
Folds
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(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
6-bladed beta-propeller
(327)
Superfamily
:
Sialidases
(238)
Family
:
Endo-alpha-sialidase
(6)
Protein domain
:
Endo-alpha-sialidase
(2)
Bacteriophage K1F [TaxId: 344021]
(2)
1a
d1v0fa1
A:245-760
1b
d1v0fe1
E:245-760
1c
d1v0ff1
F:245-760
1d
d1v0fb1
B:245-760
1e
d1v0fc1
C:245-760
1f
d1v0fd1
D:245-760
Fold
:
Triple-stranded beta-helix
(23)
Superfamily
:
Phage fibre proteins
(23)
Family
:
Endo-alpha-sialidase
(2)
Protein domain
:
Endo-alpha-sialidase
(2)
Bacteriophage K1F [TaxId: 344021]
(2)
2a
d1v0fa2
A:761-910
2b
d1v0fe2
E:761-910
2c
d1v0ff2
F:761-910
2d
d1v0fb2
B:761-910
2e
d1v0fc2
C:761-910
2f
d1v0fd2
D:761-910
[
close SCOP info
]
CATH Domains
(4, 24)
Info
all CATH domains
1a: CATH_1v0fA01 (A:245-312)
1b: CATH_1v0fD01 (D:245-311)
1c: CATH_1v0fF01 (F:245-310)
1d: CATH_1v0fC01 (C:245-312)
1e: CATH_1v0fE01 (E:245-312)
1f: CATH_1v0fB01 (B:245-311)
2a: CATH_1v0fA04 (A:756-910)
2b: CATH_1v0fD04 (D:757-910)
2c: CATH_1v0fF04 (F:757-910)
2d: CATH_1v0fC04 (C:756-910)
2e: CATH_1v0fE04 (E:756-910)
2f: CATH_1v0fB04 (B:757-910)
3a: CATH_1v0fF02 (F:311-424,F:506-756)
3b: CATH_1v0fB02 (B:312-423,B:509-756)
3c: CATH_1v0fD02 (D:312-423,D:509-756)
3d: CATH_1v0fC02 (C:313-423,C:511-755)
3e: CATH_1v0fE02 (E:313-423,E:511-755)
3f: CATH_1v0fA02 (A:313-424,A:507-755)
4a: CATH_1v0fF03 (F:425-505)
4b: CATH_1v0fB03 (B:424-508)
4c: CATH_1v0fD03 (D:424-508)
4d: CATH_1v0fA03 (A:425-506)
4e: CATH_1v0fC03 (C:424-510)
4f: CATH_1v0fE03 (E:424-510)
View:
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Classes
(
)
(
)
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)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Transcription Regulator spoIIAA
(28)
Homologous Superfamily
:
Endo-alpha-sialidase; domain 1
(2)
Coliphage k1f. Organism_taxid: 344021.
(2)
1a
1v0fA01
A:245-312
1b
1v0fD01
D:245-311
1c
1v0fF01
F:245-310
1d
1v0fC01
C:245-312
1e
1v0fE01
E:245-312
1f
1v0fB01
B:245-311
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Endosialidase, domain 4
(2)
Homologous Superfamily
:
Endosialidase, domain 4
(2)
Coliphage k1f. Organism_taxid: 344021.
(2)
2a
1v0fA04
A:756-910
2b
1v0fD04
D:757-910
2c
1v0fF04
F:757-910
2d
1v0fC04
C:756-910
2e
1v0fE04
E:756-910
2f
1v0fB04
B:757-910
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
[code=2.120.10.10, no name defined]
(150)
Coliphage k1f. Organism_taxid: 344021.
(2)
3a
1v0fF02
F:311-424,F:506-756
3b
1v0fB02
B:312-423,B:509-756
3c
1v0fD02
D:312-423,D:509-756
3d
1v0fC02
C:313-423,C:511-755
3e
1v0fE02
E:313-423,E:511-755
3f
1v0fA02
A:313-424,A:507-755
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
[code=2.40.30.20, no name defined]
(40)
Coliphage k1f. Organism_taxid: 344021.
(2)
4a
1v0fF03
F:425-505
4b
1v0fB03
B:424-508
4c
1v0fD03
D:424-508
4d
1v0fA03
A:425-506
4e
1v0fC03
C:424-510
4f
1v0fE03
E:424-510
[
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]
Pfam Domains
(0, 0)
Info
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Asym.Unit (645 KB)
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