3DH3A

Crystal structure of rluf in complex with a 22 nucleotide rna substrate
Total Genus 60
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
60
sequence length
240
structure length
240
Chain Sequence
DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEV
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Isomerase/rna
molecule keywords Ribosomal large subunit pseudouridine synthase F
total genus 60
structure length 240
sequence length 240
chains with identical sequence B, C, D
ec nomenclature ec 5.4.99.21: 23S rRNA pseudouridine(2604) synthase.
pdb deposition date 2008-06-16

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00849 PseudoU_synth_2 RNA pseudouridylate synthase
A PF01479 S4 S4 domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.10.290.10 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A RNA-binding S4 domain 3dh3A01
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 3dh3A02
4X62D 1H3FA 3HAXA 1XNQD 2F4VD 4LABA 1ZE1A 3DH3A 1J5ED 4JV5D 1N32D 5BR8D 4JI5D 2VQED 4AQYD 1HNZD 2K6PA 2UUCD 2HHHD 4X66D 4JI1D 1IBLD 1IBMD 2EY4A 1KSLA 2E5LD 4NXMD 1XMOD 4DUYD 4X65D 1V9KA 3MQKA 3T1YD 4GKJD 4LGTA 3UAIA 5LMUD 1HNWD 4B3SD 4DR3D 4DV3D 4B3RD 1JH3A 1R3EA 3LWOA 4JI2D 2AB4A 1XNRD 2VQFD 4X64D 1QYUA 1N36D 1I94D 4NXND 1XPIA 3LWRA 4OX9D 3LWQA 4YY3D 2UXBD 2UUBD 4KHPD 1P9KA 1VIOA 4LF4D 4B3TD 1R3FA 3U28A 1KSKA 2HVYA 4LF7D 4DV2D 2UU9D 4K0KD 1IBKD 3T1HD 4YHHD 4JYAD 1FKAD 1N33D 1V9FA 1ZE2A 2RFKA 4GKKD 4JI6D 1N34D 4DR1D 4JI4D 4LF9D 2AUSA 3HJYA 2KTLA 4LF6D 4DUZD 4LF8D 2ISTA 4LFAD 5IWAD 1PRZA 1KSVA 4JI3D 1K8WA 4DV4D 4LF5D 1FJGD 4DV1D 2UXDD 1C05A 1XMQD 1DM9A 4LFCD 3OTOD 4B3MD 3HP7A 1SGVA 4DV7D 1C06A 4DV0D 5LMND 4JI0D 2I82A 2UXCD 4LFBD 4DR2D 4DV5D 4JI7D 4OUDA 2UUAD 3LWVA 1HR0D 3KBGA 4JI8D 4DR6D 1HNXD 1H3EA 2ZM6D 2APOA 1ZL3A 4DV6D 4DR4D 3HJWA 4DR5D 3LWPA 4DR7D 2JANA
chains in the Genus database with same CATH superfamily
5FLXE 4X62D 1H3FA 3HAXA 4NNJA 1XNQD 2F4VD 4LABA 1ZE1A 3DH3A 1J5ED 4JV5D 1N32D 5BR8D 4JI5D 4W5VB 2VQED 4AQYD 1HNZD 2K6PA 2UUCD 2HHHD 4X66D 1SI7A 4JI1D 1IBLD 1IBMD 2EY4A 1KSLA 2E5LD 4NXMD 1XMOD 4DUYD 2I1SA 4X65D 1V9KA 3MQKA 3T1YD 4GKJD 4LGTA 3UAIA 5LMUD 1HNWD 4B3SD 4DR3D 4DV3D 4B3RD 1JH3A 1R3EA 3KYCB 3ONGA 3LWOA 4JI2D 2AB4A 1XNRD 5IT9E 3ONHA 4II2A 2VQFD 4X64D 1QYUA 1N36D 1I94D 4NXND 1XPIA 3LWRA 4OX9D 1SZWA 3LWQA 4YY3D 2UXBD 2UUBD 4KHPD 1P9KA 1VIOA 4LF4D 4B3TD 1R3FA 3U28A 1KSKA 3J7AF 2HVYA 1Y8XB 4LF7D 4DV2D 5A2QE 2UU9D 4K0KD 1IBKD 4YHHD 3T1HD 4JYAD 1FKAD 1N33D 1V9FA 1ZE2A 2RFKA 1Y8RB 4JI6D 4GKKD 1N34D 4DR1D 4JI4D 4LF9D 2AUSA 3HJYA 5FQ2B 2KTLA 4LF6D 3J81E 4DUZD 4LF8D 2ISTA 4LFAD 5IWAD 1Y8QB 3J80E 2ZTBA 1PRZA 1KSVA 4JI3D 1K8WA 4DV4D 4LF5D 1FJGD 3FN1A 4DV1D 2UXDD 1C05A 1XMQD 1DM9A 4II3A 4LFCD 3OTOD 4B3MD 1SB7A 2LQ7A 3HP7A 4DV7D 1C06A 4DV0D 1SGVA 1Z2ZA 5LMND 4JI0D 2I82A 5LL6S 2UXCD 4LFBD 4DR2D 4DV5D 4JI7D 4OUDA 2UUAD 3LWVA 1HR0D 3KBGA 4JI8D 3KYDB 2NVUB 4DR6D 3CMMA 1HNXD 3JAME 1H3EA 2ZM6D 2APOA 1ZL3A 5KNLA 4DV6D 4DR4D 3HJWA 4DR5D 3LWPA 4DR7D 2JANA
chains in the Genus database with same CATH topology
4X62D 1H3FA 3HAXA 1XNQD 2F4VD 4LABA 1ZE1A 3DH3A 1J5ED 4JV5D 1N32D 5BR8D 4JI5D 2VQED 4AQYD 1HNZD 2K6PA 2UUCD 2HHHD 4X66D 1SI7A 4JI1D 1IBLD 1IBMD 2EY4A 1KSLA 2E5LD 4NXMD 1XMOD 4DUYD 4X65D 1V9KA 3MQKA 3T1YD 4GKJD 4LGTA 3UAIA 5LMUD 1HNWD 4B3SD 4DR3D 4DV3D 4B3RD 1JH3A 1R3EA 3LWOA 4JI2D 2AB4A 1XNRD 2VQFD 4X64D 1QYUA 1N36D 1I94D 4NXND 1XPIA 3LWRA 4OX9D 1SZWA 3LWQA 4YY3D 2UXBD 2UUBD 4KHPD 1P9KA 1VIOA 4LF4D 4B3TD 1R3FA 3U28A 1KSKA 2HVYA 4LF7D 4DV2D 2UU9D 4K0KD 1IBKD 3T1HD 4YHHD 4JYAD 1FKAD 1N33D 1V9FA 1ZE2A 2RFKA 4GKKD 4JI6D 1N34D 4DR1D 4JI4D 4LF9D 2AUSA 3HJYA 2KTLA 4LF6D 4DUZD 4LF8D 2ISTA 4LFAD 5IWAD 1PRZA 1KSVA 4JI3D 1K8WA 4DV4D 4LF5D 1FJGD 4DV1D 2UXDD 1C05A 1XMQD 1DM9A 4LFCD 3OTOD 4B3MD 1SB7A 3HP7A 1SGVA 4DV7D 1C06A 4DV0D 1Z2ZA 5LMND 4JI0D 2I82A 2UXCD 4LFBD 4DR2D 4DV5D 4JI7D 4OUDA 2UUAD 3LWVA 1HR0D 3KBGA 4JI8D 4DR6D 1HNXD 1H3EA 2ZM6D 2APOA 1ZL3A 4DV6D 4DR4D 3HJWA 4DR5D 3LWPA 4DR7D 2JANA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4X62 D;  1H3F A;  3HAX A;  1XNQ D;  2F4V D;  4LAB A;  1ZE1 A;  3DH3 A;  1J5E D;  4JV5 D;  1N32 D;  5BR8 D;  4JI5 D;  2VQE D;  4AQY D;  1HNZ D;  2K6P A;  2UUC D;  2HHH D;  4X66 D;  4JI1 D;  1IBL D;  1IBM D;  2EY4 A;  1KSL A;  2E5L D;  4NXM D;  1XMO D;  4DUY D;  4X65 D;  1V9K A;  3MQK A;  3T1Y D;  4GKJ D;  4LGT A;  3UAI A;  5LMU D;  1HNW D;  4B3S D;  4DR3 D;  4DV3 D;  4B3R D;  1JH3 A;  1R3E A;  3LWO A;  4JI2 D;  2AB4 A;  1XNR D;  2VQF D;  4X64 D;  1QYU A;  1N36 D;  1I94 D;  4NXN D;  1XPI A;  3LWR A;  4OX9 D;  3LWQ A;  4YY3 D;  2UXB D;  2UUB D;  4KHP D;  1P9K A;  1VIO A;  4LF4 D;  4B3T D;  1R3F A;  3U28 A;  1KSK A;  2HVY A;  4LF7 D;  4DV2 D;  2UU9 D;  4K0K D;  1IBK D;  3T1H D;  4YHH D;  4JYA D;  1FKA D;  1N33 D;  1V9F A;  1ZE2 A;  2RFK A;  4GKK D;  4JI6 D;  1N34 D;  4DR1 D;  4JI4 D;  4LF9 D;  2AUS A;  3HJY A;  2KTL A;  4LF6 D;  4DUZ D;  4LF8 D;  2IST A;  4LFA D;  5IWA D;  1PRZ A;  1KSV A;  4JI3 D;  1K8W A;  4DV4 D;  4LF5 D;  1FJG D;  4DV1 D;  2UXD D;  1C05 A;  1XMQ D;  1DM9 A;  4LFC D;  3OTO D;  4B3M D;  3HP7 A;  1SGV A;  4DV7 D;  1C06 A;  4DV0 D;  5LMN D;  4JI0 D;  2I82 A;  2UXC D;  4LFB D;  4DR2 D;  4DV5 D;  4JI7 D;  4OUD A;  2UUA D;  3LWV A;  1HR0 D;  3KBG A;  4JI8 D;  4DR6 D;  1HNX D;  1H3E A;  2ZM6 D;  2APO A;  1ZL3 A;  4DV6 D;  4DR4 D;  3HJW A;  4DR5 D;  3LWP A;  4DR7 D;  2JAN A; 
#chains in the Genus database with same CATH topology
 5FLX E;  4X62 D;  1H3F A;  3HAX A;  4NNJ A;  1XNQ D;  2F4V D;  4LAB A;  1ZE1 A;  3DH3 A;  1J5E D;  4JV5 D;  1N32 D;  5BR8 D;  4JI5 D;  4W5V B;  2VQE D;  4AQY D;  1HNZ D;  2K6P A;  2UUC D;  2HHH D;  4X66 D;  1SI7 A;  4JI1 D;  1IBL D;  1IBM D;  2EY4 A;  1KSL A;  2E5L D;  4NXM D;  1XMO D;  4DUY D;  2I1S A;  4X65 D;  1V9K A;  3MQK A;  3T1Y D;  4GKJ D;  4LGT A;  3UAI A;  5LMU D;  1HNW D;  4B3S D;  4DR3 D;  4DV3 D;  4B3R D;  1JH3 A;  1R3E A;  3KYC B;  3ONG A;  3LWO A;  4JI2 D;  2AB4 A;  1XNR D;  5IT9 E;  3ONH A;  4II2 A;  2VQF D;  4X64 D;  1QYU A;  1N36 D;  1I94 D;  4NXN D;  1XPI A;  3LWR A;  4OX9 D;  1SZW A;  3LWQ A;  4YY3 D;  2UXB D;  2UUB D;  4KHP D;  1P9K A;  1VIO A;  4LF4 D;  4B3T D;  1R3F A;  3U28 A;  1KSK A;  3J7A F;  2HVY A;  1Y8X B;  4LF7 D;  4DV2 D;  5A2Q E;  2UU9 D;  4K0K D;  1IBK D;  4YHH D;  3T1H D;  4JYA D;  1FKA D;  1N33 D;  1V9F A;  1ZE2 A;  2RFK A;  1Y8R B;  4JI6 D;  4GKK D;  1N34 D;  4DR1 D;  4JI4 D;  4LF9 D;  2AUS A;  3HJY A;  5FQ2 B;  2KTL A;  4LF6 D;  3J81 E;  4DUZ D;  4LF8 D;  2IST A;  4LFA D;  5IWA D;  1Y8Q B;  3J80 E;  2ZTB A;  1PRZ A;  1KSV A;  4JI3 D;  1K8W A;  4DV4 D;  4LF5 D;  1FJG D;  3FN1 A;  4DV1 D;  2UXD D;  1C05 A;  1XMQ D;  1DM9 A;  4II3 A;  4LFC D;  3OTO D;  4B3M D;  1SB7 A;  2LQ7 A;  3HP7 A;  4DV7 D;  1C06 A;  4DV0 D;  1SGV A;  1Z2Z A;  5LMN D;  4JI0 D;  2I82 A;  5LL6 S;  2UXC D;  4LFB D;  4DR2 D;  4DV5 D;  4JI7 D;  4OUD A;  2UUA D;  3LWV A;  1HR0 D;  3KBG A;  4JI8 D;  3KYD B;  2NVU B;  4DR6 D;  3CMM A;  1HNX D;  3JAM E;  1H3E A;  2ZM6 D;  2APO A;  1ZL3 A;  5KNL A;  4DV6 D;  4DR4 D;  3HJW A;  4DR5 D;  3LWP A;  4DR7 D;  2JAN A; 
#chains in the Genus database with same CATH homology
 4X62 D;  1H3F A;  3HAX A;  1XNQ D;  2F4V D;  4LAB A;  1ZE1 A;  3DH3 A;  1J5E D;  4JV5 D;  1N32 D;  5BR8 D;  4JI5 D;  2VQE D;  4AQY D;  1HNZ D;  2K6P A;  2UUC D;  2HHH D;  4X66 D;  1SI7 A;  4JI1 D;  1IBL D;  1IBM D;  2EY4 A;  1KSL A;  2E5L D;  4NXM D;  1XMO D;  4DUY D;  4X65 D;  1V9K A;  3MQK A;  3T1Y D;  4GKJ D;  4LGT A;  3UAI A;  5LMU D;  1HNW D;  4B3S D;  4DR3 D;  4DV3 D;  4B3R D;  1JH3 A;  1R3E A;  3LWO A;  4JI2 D;  2AB4 A;  1XNR D;  2VQF D;  4X64 D;  1QYU A;  1N36 D;  1I94 D;  4NXN D;  1XPI A;  3LWR A;  4OX9 D;  1SZW A;  3LWQ A;  4YY3 D;  2UXB D;  2UUB D;  4KHP D;  1P9K A;  1VIO A;  4LF4 D;  4B3T D;  1R3F A;  3U28 A;  1KSK A;  2HVY A;  4LF7 D;  4DV2 D;  2UU9 D;  4K0K D;  1IBK D;  3T1H D;  4YHH D;  4JYA D;  1FKA D;  1N33 D;  1V9F A;  1ZE2 A;  2RFK A;  4GKK D;  4JI6 D;  1N34 D;  4DR1 D;  4JI4 D;  4LF9 D;  2AUS A;  3HJY A;  2KTL A;  4LF6 D;  4DUZ D;  4LF8 D;  2IST A;  4LFA D;  5IWA D;  1PRZ A;  1KSV A;  4JI3 D;  1K8W A;  4DV4 D;  4LF5 D;  1FJG D;  4DV1 D;  2UXD D;  1C05 A;  1XMQ D;  1DM9 A;  4LFC D;  3OTO D;  4B3M D;  1SB7 A;  3HP7 A;  1SGV A;  4DV7 D;  1C06 A;  4DV0 D;  1Z2Z A;  5LMN D;  4JI0 D;  2I82 A;  2UXC D;  4LFB D;  4DR2 D;  4DV5 D;  4JI7 D;  4OUD A;  2UUA D;  3LWV A;  1HR0 D;  3KBG A;  4JI8 D;  4DR6 D;  1HNX D;  1H3E A;  2ZM6 D;  2APO A;  1ZL3 A;  4DV6 D;  4DR4 D;  3HJW A;  4DR5 D;  3LWP A;  4DR7 D;  2JAN A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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