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1VDE
Asym. Unit
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Asym.Unit (150 KB)
Biol.Unit 1 (145 KB)
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(1)
Title
:
PI-SCEI, A HOMING ENDONUCLEASE WITH PROTEIN SPLICING ACTIVITY
Authors
:
X. Duan, F. A. Quiocho
Date
:
01 Apr 97 (Deposition) - 08 Apr 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Homing Endonuclease, Protein Splicing
(Keyword Search:
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)
Reference
:
X. Duan, F. S. Gimble, F. A. Quiocho
Crystal Structure Of Pi-Scei, A Homing Endonuclease With Protein Splicing Activity.
Cell(Cambridge, Mass. ) V. 89 555 1997
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
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Sorry, no Info available
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Sites
(0, 0)
Info
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: INTEIN_N_TER (A:1-83,B:1-83)
2: INTEIN_ENDONUCLEASE (A:211-359,B:211-359)
3: INTEIN_C_TER (A:430-454,B:430-454)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTEIN_N_TER
PS50817
Intein N-terminal splicing motif profile.
VATA_YEAST
284-366
2
A:1-83
B:1-83
2
INTEIN_ENDONUCLEASE
PS50819
Intein DOD-type homing endonuclease domain profile.
VATA_YEAST
494-642
2
A:211-359
B:211-359
3
INTEIN_C_TER
PS50818
Intein C-terminal splicing motif profile.
VATA_YEAST
713-738
2
A:430-454
B:430-454
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Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:1-454 (gaps) | B:1-454 (gaps))
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YDL185W
1
YDL185W.1
IV:126788-130003
3216
VATA_YEAST
1-1071
1071
2
A:1-454 (gaps)
B:1-454 (gaps)
454
454
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SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1vdea1 (A:1-180,A:416-454)
1b: SCOP_d1vdeb1 (B:1-180,B:416-454)
2a: SCOP_d1vdea2 (A:181-298)
2b: SCOP_d1vdea3 (A:299-415)
2c: SCOP_d1vdeb2 (B:181-298)
2d: SCOP_d1vdeb3 (B:299-415)
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Protein Domains
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Class
:
All beta proteins
(24004)
Fold
:
Hedgehog/intein (Hint) domain
(16)
Superfamily
:
Hedgehog/intein (Hint) domain
(16)
Family
:
Intein (protein splicing domain)
(12)
Protein domain
:
VMA1-derived endonuclease (VDE) PI-Scei intein
(8)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(8)
1a
d1vdea1
A:1-180,A:416-454
1b
d1vdeb1
B:1-180,B:416-454
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Homing endonuclease-like
(42)
Superfamily
:
Homing endonucleases
(38)
Family
:
Intein endonuclease
(8)
Protein domain
:
VMA1-derived endonuclease (VDE) PI-SceI
(7)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
2a
d1vdea2
A:181-298
2b
d1vdea3
A:299-415
2c
d1vdeb2
B:181-298
2d
d1vdeb3
B:299-415
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1vdeA02 (A:183-303)
1b: CATH_1vdeB02 (B:183-303)
1c: CATH_1vdeA03 (A:304-398)
1d: CATH_1vdeB03 (B:304-398)
2a: CATH_1vdeA01 (A:1-179,A:416-454)
2b: CATH_1vdeB01 (B:1-179,B:416-454)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Endonuclease I-creI
(41)
Homologous Superfamily
:
Homing endonucleases
(40)
Baker's yeast (Saccharomyces cerevisiae)
(8)
1a
1vdeA02
A:183-303
1b
1vdeB02
B:183-303
1c
1vdeA03
A:304-398
1d
1vdeB03
B:304-398
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Endonuclease - Pi-scei; Chain A, domain 1
(12)
Homologous Superfamily
:
Endonuclease - Pi-scei; Chain A, domain 1
(12)
Baker's yeast (Saccharomyces cerevisiae)
(6)
2a
1vdeA01
A:1-179,A:416-454
2b
1vdeB01
B:1-179,B:416-454
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Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_Hom_end_hint_1vdeB01 (B:1-454)
1b: PFAM_Hom_end_hint_1vdeB02 (B:1-454)
2a: PFAM_Hom_end_1vdeB03 (B:302-413)
2b: PFAM_Hom_end_1vdeB04 (B:302-413)
2c: PFAM_Hom_end_1vdeB05 (B:302-413)
2d: PFAM_Hom_end_1vdeB06 (B:302-413)
3a: PFAM_ATP_synt_ab_1vdeB07 (B:1-454)
3b: PFAM_ATP_synt_ab_1vdeB08 (B:1-454)
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Clan
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H-int
(15)
Family
:
Hom_end_hint
(5)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
1a
Hom_end_hint-1vdeB01
B:1-454
1b
Hom_end_hint-1vdeB02
B:1-454
Clan
:
Homing_endonuc
(19)
Family
:
Hom_end
(5)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
2a
Hom_end-1vdeB03
B:302-413
2b
Hom_end-1vdeB04
B:302-413
2c
Hom_end-1vdeB05
B:302-413
2d
Hom_end-1vdeB06
B:302-413
Clan
:
P-loop_NTPase
(1112)
Family
:
ATP-synt_ab
(44)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(11)
3a
ATP-synt_ab-1vdeB07
B:1-454
3b
ATP-synt_ab-1vdeB08
B:1-454
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