3U28A

Crystal structure of a cbf5-nop10-gar1 complex from saccharomyces cerevisiae
Total Genus 102

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
102
sequence length
346
structure length
335
Chain Sequence
DFVIKPEDTSEWPLLLKNFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVCIVRLHDALKDEKDLGRSLENLTGALFQRPPKRQLRVRTIYESNLIEFDNKRNLGVFWASCEAGTYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRW
5010015020025030030025020015010050
020406080100Genus Matrix

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
EMPTYO1 (5-7)3H2 (29-31)S14 (290-293)TI1 (19-22)AH8 (276-282)3H1 (24-26)TI7 (307-310)S16 (312-318)S11 (256-258)S1 (33-34)TII3 (294-297)TVIII1 (34-37)3H3 (48-50)AH6 (233-246)AH1 (53-58)AH5 (196-207)S2 (59-66)AH2 (72-83)TIV3 (227-230)S4 (99-107)3H4 (108-112)S3 (88-90)TIV2 (207-210)S5 (121-129)TVIII2 (133-136)AH4 (137-146)TIV1 (154-162)TI3 (178-181)S6 (148-152)S7 (165-178)S8 (183-190)TI4 (179-182)S10 (224-225)TI5 (225-228)AH7 (249-255)S13 (284-286)3H6 (273-275)S12 (268-271)TI6 (263-266)AH9 (322-327)3H7 (287-289)S15 (301-306)TIV4 (318-321)S9 (211-221)TI2 (95-98)TII'1 (221-224)3H5 (259-262)TII4 (298-301)AH3 (113-118)TII2 (191-194)Updating...
connected with : NaN
molecule tags Isomerase/protein binding
source organism Saccharomyces cerevisiae
publication title Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase
pubmed doi rcsb
molecule keywords H/ACA ribonucleoprotein complex subunit 4
total genus 102
structure length 335
sequence length 346
ec nomenclature ec 5.4.99.-:
pdb deposition date 2011-10-02

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01472 PUA PUA domain
A PF01509 TruB_N TruB family pseudouridylate synthase (N terminal domain)
A PF08068 DKCLD DKCLD (NUC011) domain
A PF16198 TruB_C_2 tRNA pseudouridylate synthase B C-terminal domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.30.130.70 Mainly Beta Roll Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 3u28A01
3.30.2350.10 Alpha Beta 2-Layer Sandwich Pseudouridine synthase Pseudouridine synthase 3u28A02
4LGTA 1V9FA 3HAXA 1PRZA 2AUSA 1SGVA 1ZE2A 1R3EA 1ZE1A 1KSLA 1XPIA 2EY4A 3HJWA 4LABA 1KSVA 3U28A 3ZV0C 3HJYA 3LWRA 2APOA 3UAIA 2HVYA 1QYUA 3LWOA 1ZL3A 3MQKA 1K8WA 2AB4A 1KSKA 3LWPA 2ISTA 3LWVA 3LWQA 2I82A 1R3FA 1V9KA 3DH3A 2RFKA
chains in the Genus database with same CATH superfamily
2FRXA 1SGVA 1WXXA 1IT8A 1IQ8A 1KSLA 4DMGA 4CI1B 3M65A 3HJYA 4CI3B 2APOA 3LWOA 1KSKA 2CWWA 2Z0TA 3LWVA 2DP9A 2P38A 3C0KA 1IT7A 1TE7A 2AS0A 1UOYA 4LGTA 3HAXA 1PRZA 1ZE1A 1SZWA 3D79A 1SI7A 1SB7A 2CX0A 3M6UA 4Q1TA 3M4XA 1KSVA 3ZV0C 2J5VA 3UAIA 2KKUA 2E5OA 1ZL3A 1K8WA 3LWPA 3LJCA 3LWQA 1Z2ZA 1SQWA 1ZS7A 2J5TA 2RFKA 1Q7HA 3M6WA 1ZE2A 1R3EA 1XNEA 1ZBOA 2Q07A 1XPIA 3M6XA 2EY4A 3HJWA 3LDFA 1J2BA 3U28A 4CI2B 4TZ4C 1QYUA 2AB4A 3VSEA 2I82A 1S04A 3DH3A 1WK2A 1V9FA 2AUSA 3M6VA 4LABA 3LWRA 2HVYA 2ANEA 3MQKA 2B78A 3IUWA 2CX1A 2ISTA 1WXWA 1R3FA 1T5YA 1V9KA
chains in the Genus database with same CATH topology
2FRXA 3M6WA 1UOYA 1V9FA 3HAXA 1PRZA 2AUSA 1SGVA 4LGTA 1ZE2A 1ZE1A 3M6VA 1R3EA 1SZWA 1KSLA 1XPIA 3M6XA 2EY4A 1SB7A 3HJWA 1SI7A 4LABA 3M6UA 3M4XA 1KSVA 3U28A 3ZV0C 3HJYA 3LWRA 2APOA 3UAIA 2HVYA 1QYUA 3LWOA 1ZL3A 3MQKA 1K8WA 2AB4A 1KSKA 3LWPA 2ISTA 3LWVA 3LWQA 1Z2ZA 2I82A 1R3FA 1V9KA 3DH3A 2RFKA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4LGT A;  1V9F A;  3HAX A;  1PRZ A;  2AUS A;  1SGV A;  1ZE2 A;  1R3E A;  1ZE1 A;  1KSL A;  1XPI A;  2EY4 A;  3HJW A;  4LAB A;  1KSV A;  3U28 A;  3ZV0 C;  3HJY A;  3LWR A;  2APO A;  3UAI A;  2HVY A;  1QYU A;  3LWO A;  1ZL3 A;  3MQK A;  1K8W A;  2AB4 A;  1KSK A;  3LWP A;  2IST A;  3LWV A;  3LWQ A;  2I82 A;  1R3F A;  1V9K A;  3DH3 A;  2RFK A; 
#chains in the Genus database with same CATH topology
 2FRX A;  1SGV A;  1WXX A;  1IT8 A;  1IQ8 A;  1KSL A;  4DMG A;  4CI1 B;  3M65 A;  3HJY A;  4CI3 B;  2APO A;  3LWO A;  1KSK A;  2CWW A;  2Z0T A;  3LWV A;  2DP9 A;  2P38 A;  3C0K A;  1IT7 A;  1TE7 A;  2AS0 A;  1UOY A;  4LGT A;  3HAX A;  1PRZ A;  1ZE1 A;  1SZW A;  3D79 A;  1SI7 A;  1SB7 A;  2CX0 A;  3M6U A;  4Q1T A;  3M4X A;  1KSV A;  3ZV0 C;  2J5V A;  3UAI A;  2KKU A;  2E5O A;  1ZL3 A;  1K8W A;  3LWP A;  3LJC A;  3LWQ A;  1Z2Z A;  1SQW A;  1ZS7 A;  2J5T A;  2RFK A;  1Q7H A;  3M6W A;  1ZE2 A;  1R3E A;  1XNE A;  1ZBO A;  2Q07 A;  1XPI A;  3M6X A;  2EY4 A;  3HJW A;  3LDF A;  1J2B A;  3U28 A;  4CI2 B;  4TZ4 C;  1QYU A;  2AB4 A;  3VSE A;  2I82 A;  1S04 A;  3DH3 A;  1WK2 A;  1V9F A;  2AUS A;  3M6V A;  4LAB A;  3LWR A;  2HVY A;  2ANE A;  3MQK A;  2B78 A;  3IUW A;  2CX1 A;  2IST A;  1WXW A;  1R3F A;  1T5Y A;  1V9K A; 
#chains in the Genus database with same CATH homology
 2FRX A;  3M6W A;  1UOY A;  1V9F A;  3HAX A;  1PRZ A;  2AUS A;  1SGV A;  4LGT A;  1ZE2 A;  1ZE1 A;  3M6V A;  1R3E A;  1SZW A;  1KSL A;  1XPI A;  3M6X A;  2EY4 A;  1SB7 A;  3HJW A;  1SI7 A;  4LAB A;  3M6U A;  3M4X A;  1KSV A;  3U28 A;  3ZV0 C;  3HJY A;  3LWR A;  2APO A;  3UAI A;  2HVY A;  1QYU A;  3LWO A;  1ZL3 A;  3MQK A;  1K8W A;  2AB4 A;  1KSK A;  3LWP A;  2IST A;  3LWV A;  3LWQ A;  1Z2Z A;  2I82 A;  1R3F A;  1V9K A;  3DH3 A;  2RFK A; 
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similar chains in the pdb database (?% sequence similarity)

 
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