PDB: 1jva Compound: vma1-derived homing endonuclease x10sss Classification: HYDROLASE Entry date in PDB: 2002-08-29 Resolution [Å]: 2.10 R-Factor: 0.198

CHAIN: A SWISS-PROT/TREMBL: P17255    KEYWORD: 3D-structure    ATP synthesis    ATP-binding    Autocatalytic cleavage    DNA-binding    Endonuclease    Hydrogen ion transport    Hydrolase    Intron homing    Nuclease    Protein splicing    EC: 3.6.3.14 SCOP: b.86.1.2 All beta proteins    Hedgehog/intein (Hint) domain    Hedgehog/intein (Hint) domain    Intein (protein splicing domain)    VMA1-derived endonuclease (VDE) PI-Scei intein    Baker's yeast (Saccharomyces cerevisiae) SCOP: b.86.1.2 All beta proteins    Hedgehog/intein (Hint) domain    Hedgehog/intein (Hint) domain    Intein (protein splicing domain)    VMA1-derived endonuclease (VDE) PI-Scei intein    Baker's yeast (Saccharomyces cerevisiae) SCOP: d.95.2.2 Alpha and beta proteins (a+b)    Homing endonuclease-like    Homing endonucleases    Intein endonuclease    VMA1-derived endonuclease (VDE) PI-SceI    Baker's yeast (Saccharomyces cerevisiae) SCOP: d.95.2.2 Alpha and beta proteins (a+b)    Homing endonuclease-like    Homing endonucleases    Intein endonuclease    VMA1-derived endonuclease (VDE) PI-SceI    Baker's yeast (Saccharomyces cerevisiae) GO:  proton-transporting two-sector ATPase complex    ATP binding    DNA binding    endonuclease activity    hydrogen-transporting ATP synthase activity, rotational mechanism    hydrogen-transporting ATPase activity, rotational mechanism    ATP biosynthesis    ATP synthesis coupled proton transport    intein-mediated protein splicing    protein splicing    CHAIN: B SWISS-PROT/TREMBL: P17255    KEYWORD: 3D-structure    ATP synthesis    ATP-binding    Autocatalytic cleavage    DNA-binding    Endonuclease    Hydrogen ion transport    Hydrolase    Intron homing    Nuclease    Protein splicing    EC: 3.6.3.14 SCOP: b.86.1.2 All beta proteins    Hedgehog/intein (Hint) domain    Hedgehog/intein (Hint) domain    Intein (protein splicing domain)    VMA1-derived endonuclease (VDE) PI-Scei intein    Baker's yeast (Saccharomyces cerevisiae) SCOP: b.86.1.2 All beta proteins    Hedgehog/intein (Hint) domain    Hedgehog/intein (Hint) domain    Intein (protein splicing domain)    VMA1-derived endonuclease (VDE) PI-Scei intein    Baker's yeast (Saccharomyces cerevisiae) SCOP: d.95.2.2 Alpha and beta proteins (a+b)    Homing endonuclease-like    Homing endonucleases    Intein endonuclease    VMA1-derived endonuclease (VDE) PI-SceI    Baker's yeast (Saccharomyces cerevisiae) SCOP: d.95.2.2 Alpha and beta proteins (a+b)    Homing endonuclease-like    Homing endonucleases    Intein endonuclease    VMA1-derived endonuclease (VDE) PI-SceI    Baker's yeast (Saccharomyces cerevisiae) GO:  proton-transporting two-sector ATPase complex    ATP binding    DNA binding    endonuclease activity    hydrogen-transporting ATP synthase activity, rotational mechanism    hydrogen-transporting ATPase activity, rotational mechanism    ATP biosynthesis    ATP synthesis coupled proton transport    intein-mediated protein splicing    protein splicing

Image Source: PDB

Loops in ArchDB40 clusters

1jva_A_627 - HE => SUBCLASS : 1.1.1
1jva_A_516 - HE => SUBCLASS : 1.1.4
1jva_A_516 - HE => SUBCLASS : 1.1.6
1jva_A_516 - HE => SUBCLASS : 1.1.7
1jva_A_452 - HE => SUBCLASS : 1.2.10
1jva_A_568 - HE => SUBCLASS : 2.4.1
1jva_A_309 - HA => SUBCLASS : 3.1.1
1jva_A_609 - HA => SUBCLASS : 4.23.1
1jva_A_619 - EH => SUBCLASS : 2.1.1
1jva_A_508 - EH => SUBCLASS : 3.1.1
1jva_A_285 - AR => SUBCLASS : 1.2.1
1jva_A_285 - AR => SUBCLASS : 3.1.1
1jva_A_285 - AR => SUBCLASS : 3.3.1
1jva_A_355 - AR => SUBCLASS : 3.7.1

Loops in ArchDB95 clusters

1jva_A_619 - EH => SUBCLASS : 2.1.2
1jva_A_508 - EH => SUBCLASS : 3.2.1
1jva_A_508 - EH => SUBCLASS : 3.2.3
1jva_A_285 - AR => SUBCLASS : 1.1.4
1jva_A_355 - AR => SUBCLASS : 2.2.1
1jva_A_285 - AR => SUBCLASS : 3.3.2
1jva_A_309 - HA => SUBCLASS : 3.1.1
1jva_A_609 - HA => SUBCLASS : 7.19.1

Loops in ArchDB-EC clusters

1jva_A_568 - HE => SUBCLASS : 2.3.3

Loops not clustered in ArchDB

1jva_A_298 - AR
1jva_A_317 - AR
1jva_A_363 - AR
1jva_A_363 - AR
1jva_A_355 - AR
1jva_A_700 - AR
1jva_A_704 - AR
1jva_A_317 - AR
1jva_A_285 - AR
1jva_A_298 - AR
1jva_A_704 - AR
1jva_A_700 - AR
1jva_A_583 - EH
1jva_A_544 - EH
1jva_A_402 - EH
1jva_A_460 - EH
1jva_A_437 - EH
1jva_A_663 - EH
1jva_A_309 - HA
1jva_A_325 - HA
1jva_A_726 - HA
1jva_A_372 - HA
1jva_A_382 - HA
1jva_A_532 - HA
1jva_A_643 - HA
1jva_A_579 - HA
1jva_A_609 - HA
1jva_A_290 - HA
1jva_A_290 - HA
1jva_A_325 - HA
1jva_A_372 - HA
1jva_A_382 - HA
1jva_A_532 - HA
1jva_A_579 - HA
1jva_A_643 - HA
1jva_A_726 - HA
1jva_A_672 - HE
1jva_A_595 - HE
1jva_A_487 - HE
1jva_A_420 - HE
1jva_A_471 - HH

1dfa A - percentage of sequence identity: 99
1ef0 A - percentage of sequence identity: 99
1ef0 B - percentage of sequence identity: 99
1gpp A - percentage of sequence identity: 97
1jva A - percentage of sequence identity: 100
1jva B - percentage of sequence identity: 100
1lws A - percentage of sequence identity: 99
1lwt A - percentage of sequence identity: 99
1um2 A - percentage of sequence identity: 99
1um2 B - percentage of sequence identity: 99
1vde A - percentage of sequence identity: 99
1vde B - percentage of sequence identity: 99