2YBRC

Crystal structure of the human derived single chain antibody fragment (scfv) 9004g in complex with cn2 toxin from the scorpion centruroides noxius hoffmann
Total Genus 15
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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
15
sequence length
65
structure length
65
Chain Sequence
KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRC
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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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molecule keywords SINGLE CHAIN ANTIBODY FRAGMENT 9004G
publication title Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides Noxius Hoffmann by a Human-Derived Single Chain Antibody Fragment
pubmed doi rcsb
source organism Homo sapiens
molecule tags Immune system/toxin
total genus 15
structure length 65
sequence length 65
chains with identical sequence F, I
ec nomenclature
pdb deposition date 2011-03-09

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
C PF00537 Toxin_3 Scorpion toxin-like domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.30.10 Alpha Beta 2-Layer Sandwich Defensin A-like Knottin, scorpion toxin-like 2ybrC00
3E7UX 4UJ0A 1C55A 1ZYVA 3E7RL 2ASCA 1T7AA 1JZBA 4V1DC 5CY0A 2LY5A 1LQQA 2E3GA 1DJTA 2KBKA 2N2RA 1T0ZA 1P0AA 1GPTA 1ZUTA 1JXCA 1NH5A 1SNBA 1AYJA 1OZZA 1PE4A 1ZVGA 1TI5A 2YC1C 1ZVEA 2LR3A 1NE5A 1PX9A 1LQHA 1C56A 2KPYA 2LJMA 1B3CA 1PTXA 2B3CA 4CQKA 1KV0A 1MR4A 2I61A 2LY6A 2BRZA 1WWNA 1L4VA 2B68A 4HHFA 1NRBA 1ZYWA 2KYQA 2N2QA 1WMTA 2YBRC 2M8BB 1NPIA 1BCGA 2NY9X 2KBHA 1AHOA 3PSMA 1I2VA 1OMYA 2KGQA 2E0HA 1I6FA 1P00A 2LT8A 1CHZA 1T7BA 2YEOA 1I6GA 1SN4A 1WT7A 2MZ0A 1MYNA 1NRAA 2KBJA 1T7EA 1BRZA 2GL1A 2ATBA 1I2UA 1VNBA 1GPSA 2E3FA 2KJAA 2A7TA 2SN3A 1LQIA 4HE7A 1ZFUA 1BMRA 1DQ7A 1ICAA 1CN2A 2LKBA 4AB0A 4KYPA 1ZU3A 4AEIA 1SN1A 2KSKA 2LI7A 1T1TA 5KK4A 4AAZA 2N66A 1BK8A 1JKZA 1VNAA 1JZAA 1N4NA 2N69A 1FH3A 1SEGA 2LJ7A 1B7DA 2NY8X
chains in the Genus database with same CATH superfamily
5AQYA 2MBKA 1HJOA 2YILA 3E7UX 5F0XA 4UJ0A 2K35A 1C55A 1ZYVA 2YIOA 1BA0A 2V7ZA 3E7RL 2ASCA 3L6QA 1BA1A 1T7AA 5AQGA 1JZBA 3D2EA 4V1DC 5CY0A 2LY5A 1LQQA 5AQLA 2LN8A 1NGCA 2E3GA 1DJTA 2QWOA 1NGAA 2E8AA 1QQOA 2KBKA 1KAYA 1NGHA 2N2RA 5FPDA 1NGDA 5AR0A 5FPNA 5BPLA 1T0ZA 1UGLA 4UAFE 1P0AA 2D56A 3FE1A 4HWIA 5AQIA 5AQXA 1GPTA 5AQVA 3LDQA 1ZUTA 5FPEA 3QFUA 1JXCA 1NH5A 2GMOA 1SNBA 5AQFA 3KOXA 3M3ZA 1AYJA 2QWPA 1OZZA 1PE4A 3HSCA 4H5RA 1ZVGA 1TI5A 2YC1C 2JDQD 1ZVEA 2LR3A 3LDLA 3QFPA 5AQKA 5AQPA 1NE5A 5FPMA 1PX9A 1LQHA 1C56A 2KPYA 2LJMA 5EXWA 1B3CA 5BPNA 1PTXA 1XRSB 2QWQA 2B3CA 4CQKA 1KV0A 1MR4A 2I61A 3KP0A 2LY6A 2BRZA 3FZFA 3IUCA 1WWNA 1ATRA 2E88A 3ATVA 4FL9A 2B68A 4HHFA 1L4VA 2QWRA 1NRBA 5F1XA 3QMLA 1KAXA 1ZYWA 5EY4A 1QQMA 3FZKA 2KYQA 2N2QA 1DKGD 1HPMA 1WMTA 3CQXA 1S3XA 3D2FB 2YBRC 1NGIA 5BPMA 2M8BB 3C7NB 3KC6A 3GDQA 1NPIA 1BCGA 2NY9X 4H5TA 2KBHA 1AHOA 3BK3C 3PSMA 3KHWA 3LDNA 1OMYA 3AY9A 1I2VA 2KGQA 2QW9A 3LDPA 2E0HA 3FZHA 1I6FA 2KHOA 3JXUA 1NGGA 2E2FA 4FSVA 1P00A 2LT8A 1CHZA 1T7BA 2MN5A 2YEOA 4GNIA 1I6GA 1SN4A 1WT7A 2MZ0A 2YIPA 1MYNA 5AQTA 5AQOA 2G2KA 1NGBA 5BN9A 3D2FA 1QQNA 3I33A 3R2VA 3C7NA 5AQWA 3CW4A 1NRAA 2KBJA 3KOYA 3KOZA 4H5WA 1T7EA 1BRZA 2GL1A 2ATBA 3ATUA 1VNBA 3L4IA 1GPSA 2E3FA 1I2UA 2KJAA 2A7TA 1KAZA 2SN3A 5AQNA 5AQZA 5BN8A 1LQIA 3LDOA 4UAEF 5AQJA 4HE7A 1ZFUA 2QWMA 3FZMA 1BMRA 1DQ7A 1ICAA 2QWNA 1CN2A 1K8BA 3FZLA 3GL1A 2LKBA 3L56A 1YUWA 4AB0A 2QXLA 4KYPA 1NGFA 1ZU3A 4KBOA 2QWLA 4AEIA 1NGEA 5EX5A 3QI7A 4H5VA 5EVZA 1BUPA 1POIA 1SN1A 1ATSA 5AQUA 3SF4D 3KP1A 2KSKA 2LI7A 1T1TA 3D2EB 5KK4A 1HX1A 4AAZA 3GKUA 2N66A 5AQRA 1BK8A 4UADE 1JKZA 1VNAA 3KOWA 1JZAA 2BUPA 4IO8A 5AQQA 3A8YA 1N4NA 3KVGA 5F2RA 2N69A 2VY6A 1SEGA 4H5NA 1FH3A 2LJ7A 5AQSA 1B7DA 5AQMA 1NGJA 5AQHA 2NY8X
chains in the Genus database with same CATH topology
3E7UX 4UJ0A 1C55A 1ZYVA 3E7RL 2ASCA 1T7AA 1JZBA 4V1DC 5CY0A 2LY5A 1LQQA 2E3GA 1DJTA 2KBKA 2N2RA 1T0ZA 1P0AA 1GPTA 1ZUTA 1JXCA 1NH5A 1SNBA 1AYJA 1OZZA 1PE4A 1ZVGA 1TI5A 2YC1C 1ZVEA 2LR3A 1NE5A 1PX9A 1LQHA 1C56A 2KPYA 2LJMA 1B3CA 1PTXA 2B3CA 4CQKA 1KV0A 1MR4A 2I61A 2LY6A 2BRZA 1WWNA 1L4VA 2B68A 4HHFA 1NRBA 1ZYWA 2KYQA 2N2QA 1WMTA 2YBRC 2M8BB 1NPIA 1BCGA 2NY9X 2KBHA 1AHOA 3PSMA 1I2VA 1OMYA 2KGQA 2E0HA 1I6FA 1P00A 2LT8A 1CHZA 1T7BA 2YEOA 1I6GA 1SN4A 1WT7A 2MZ0A 1MYNA 1NRAA 2KBJA 1T7EA 1BRZA 2GL1A 2ATBA 1I2UA 1VNBA 1GPSA 2E3FA 2KJAA 2A7TA 2SN3A 1LQIA 4HE7A 1ZFUA 1BMRA 1DQ7A 1ICAA 1CN2A 2LKBA 4AB0A 4KYPA 1ZU3A 4AEIA 1SN1A 2KSKA 2LI7A 1T1TA 5KK4A 4AAZA 2N66A 1BK8A 1JKZA 1VNAA 1JZAA 1N4NA 2N69A 1FH3A 1SEGA 2LJ7A 1B7DA 2NY8X
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3E7U X;  4UJ0 A;  1C55 A;  1ZYV A;  3E7R L;  2ASC A;  1T7A A;  1JZB A;  4V1D C;  5CY0 A;  2LY5 A;  1LQQ A;  2E3G A;  1DJT A;  2KBK A;  2N2R A;  1T0Z A;  1P0A A;  1GPT A;  1ZUT A;  1JXC A;  1NH5 A;  1SNB A;  1AYJ A;  1OZZ A;  1PE4 A;  1ZVG A;  1TI5 A;  2YC1 C;  1ZVE A;  2LR3 A;  1NE5 A;  1PX9 A;  1LQH A;  1C56 A;  2KPY A;  2LJM A;  1B3C A;  1PTX A;  2B3C A;  4CQK A;  1KV0 A;  1MR4 A;  2I61 A;  2LY6 A;  2BRZ A;  1WWN A;  1L4V A;  2B68 A;  4HHF A;  1NRB A;  1ZYW A;  2KYQ A;  2N2Q A;  1WMT A;  2YBR C;  2M8B B;  1NPI A;  1BCG A;  2NY9 X;  2KBH A;  1AHO A;  3PSM A;  1I2V A;  1OMY A;  2KGQ A;  2E0H A;  1I6F A;  1P00 A;  2LT8 A;  1CHZ A;  1T7B A;  2YEO A;  1I6G A;  1SN4 A;  1WT7 A;  2MZ0 A;  1MYN A;  1NRA A;  2KBJ A;  1T7E A;  1BRZ A;  2GL1 A;  2ATB A;  1I2U A;  1VNB A;  1GPS A;  2E3F A;  2KJA A;  2A7T A;  2SN3 A;  1LQI A;  4HE7 A;  1ZFU A;  1BMR A;  1DQ7 A;  1ICA A;  1CN2 A;  2LKB A;  4AB0 A;  4KYP A;  1ZU3 A;  4AEI A;  1SN1 A;  2KSK A;  2LI7 A;  1T1T A;  5KK4 A;  4AAZ A;  2N66 A;  1BK8 A;  1JKZ A;  1VNA A;  1JZA A;  1N4N A;  2N69 A;  1FH3 A;  1SEG A;  2LJ7 A;  1B7D A;  2NY8 X; 
#chains in the Genus database with same CATH topology
 5AQY A;  2MBK A;  1HJO A;  2YIL A;  3E7U X;  5F0X A;  4UJ0 A;  2K35 A;  1C55 A;  1ZYV A;  2YIO A;  1BA0 A;  2V7Z A;  3E7R L;  2ASC A;  3L6Q A;  1BA1 A;  1T7A A;  5AQG A;  1JZB A;  3D2E A;  4V1D C;  5CY0 A;  2LY5 A;  1LQQ A;  5AQL A;  2LN8 A;  1NGC A;  2E3G A;  1DJT A;  2QWO A;  1NGA A;  2E8A A;  1QQO A;  2KBK A;  1KAY A;  1NGH A;  2N2R A;  5FPD A;  1NGD A;  5AR0 A;  5FPN A;  5BPL A;  1T0Z A;  1UGL A;  4UAF E;  1P0A A;  2D56 A;  3FE1 A;  4HWI A;  5AQI A;  5AQX A;  1GPT A;  5AQV A;  3LDQ A;  1ZUT A;  5FPE A;  3QFU A;  1JXC A;  1NH5 A;  2GMO A;  1SNB A;  5AQF A;  3KOX A;  3M3Z A;  1AYJ A;  2QWP A;  1OZZ A;  1PE4 A;  3HSC A;  4H5R A;  1ZVG A;  1TI5 A;  2YC1 C;  2JDQ D;  1ZVE A;  2LR3 A;  3LDL A;  3QFP A;  5AQK A;  5AQP A;  1NE5 A;  5FPM A;  1PX9 A;  1LQH A;  1C56 A;  2KPY A;  2LJM A;  5EXW A;  1B3C A;  5BPN A;  1PTX A;  1XRS B;  2QWQ A;  2B3C A;  4CQK A;  1KV0 A;  1MR4 A;  2I61 A;  3KP0 A;  2LY6 A;  2BRZ A;  3FZF A;  3IUC A;  1WWN A;  1ATR A;  2E88 A;  3ATV A;  4FL9 A;  2B68 A;  4HHF A;  1L4V A;  2QWR A;  1NRB A;  5F1X A;  3QML A;  1KAX A;  1ZYW A;  5EY4 A;  1QQM A;  3FZK A;  2KYQ A;  2N2Q A;  1DKG D;  1HPM A;  1WMT A;  3CQX A;  1S3X A;  3D2F B;  2YBR C;  1NGI A;  5BPM A;  2M8B B;  3C7N B;  3KC6 A;  3GDQ A;  1NPI A;  1BCG A;  2NY9 X;  4H5T A;  2KBH A;  1AHO A;  3BK3 C;  3PSM A;  3KHW A;  3LDN A;  1OMY A;  3AY9 A;  1I2V A;  2KGQ A;  2QW9 A;  3LDP A;  2E0H A;  3FZH A;  1I6F A;  2KHO A;  3JXU A;  1NGG A;  2E2F A;  4FSV A;  1P00 A;  2LT8 A;  1CHZ A;  1T7B A;  2MN5 A;  2YEO A;  4GNI A;  1I6G A;  1SN4 A;  1WT7 A;  2MZ0 A;  2YIP A;  1MYN A;  5AQT A;  5AQO A;  2G2K A;  1NGB A;  5BN9 A;  3D2F A;  1QQN A;  3I33 A;  3R2V A;  3C7N A;  5AQW A;  3CW4 A;  1NRA A;  2KBJ A;  3KOY A;  3KOZ A;  4H5W A;  1T7E A;  1BRZ A;  2GL1 A;  2ATB A;  3ATU A;  1VNB A;  3L4I A;  1GPS A;  2E3F A;  1I2U A;  2KJA A;  2A7T A;  1KAZ A;  2SN3 A;  5AQN A;  5AQZ A;  5BN8 A;  1LQI A;  3LDO A;  4UAE F;  5AQJ A;  4HE7 A;  1ZFU A;  2QWM A;  3FZM A;  1BMR A;  1DQ7 A;  1ICA A;  2QWN A;  1CN2 A;  1K8B A;  3FZL A;  3GL1 A;  2LKB A;  3L56 A;  1YUW A;  4AB0 A;  2QXL A;  4KYP A;  1NGF A;  1ZU3 A;  4KBO A;  2QWL A;  4AEI A;  1NGE A;  5EX5 A;  3QI7 A;  4H5V A;  5EVZ A;  1BUP A;  1POI A;  1SN1 A;  1ATS A;  5AQU A;  3SF4 D;  3KP1 A;  2KSK A;  2LI7 A;  1T1T A;  3D2E B;  5KK4 A;  1HX1 A;  4AAZ A;  3GKU A;  2N66 A;  5AQR A;  1BK8 A;  4UAD E;  1JKZ A;  1VNA A;  3KOW A;  1JZA A;  2BUP A;  4IO8 A;  5AQQ A;  3A8Y A;  1N4N A;  3KVG A;  5F2R A;  2N69 A;  2VY6 A;  1SEG A;  4H5N A;  1FH3 A;  2LJ7 A;  5AQS A;  1B7D A;  5AQM A;  1NGJ A;  5AQH A;  2NY8 X; 
#chains in the Genus database with same CATH homology
 3E7U X;  4UJ0 A;  1C55 A;  1ZYV A;  3E7R L;  2ASC A;  1T7A A;  1JZB A;  4V1D C;  5CY0 A;  2LY5 A;  1LQQ A;  2E3G A;  1DJT A;  2KBK A;  2N2R A;  1T0Z A;  1P0A A;  1GPT A;  1ZUT A;  1JXC A;  1NH5 A;  1SNB A;  1AYJ A;  1OZZ A;  1PE4 A;  1ZVG A;  1TI5 A;  2YC1 C;  1ZVE A;  2LR3 A;  1NE5 A;  1PX9 A;  1LQH A;  1C56 A;  2KPY A;  2LJM A;  1B3C A;  1PTX A;  2B3C A;  4CQK A;  1KV0 A;  1MR4 A;  2I61 A;  2LY6 A;  2BRZ A;  1WWN A;  1L4V A;  2B68 A;  4HHF A;  1NRB A;  1ZYW A;  2KYQ A;  2N2Q A;  1WMT A;  2YBR C;  2M8B B;  1NPI A;  1BCG A;  2NY9 X;  2KBH A;  1AHO A;  3PSM A;  1I2V A;  1OMY A;  2KGQ A;  2E0H A;  1I6F A;  1P00 A;  2LT8 A;  1CHZ A;  1T7B A;  2YEO A;  1I6G A;  1SN4 A;  1WT7 A;  2MZ0 A;  1MYN A;  1NRA A;  2KBJ A;  1T7E A;  1BRZ A;  2GL1 A;  2ATB A;  1I2U A;  1VNB A;  1GPS A;  2E3F A;  2KJA A;  2A7T A;  2SN3 A;  1LQI A;  4HE7 A;  1ZFU A;  1BMR A;  1DQ7 A;  1ICA A;  1CN2 A;  2LKB A;  4AB0 A;  4KYP A;  1ZU3 A;  4AEI A;  1SN1 A;  2KSK A;  2LI7 A;  1T1T A;  5KK4 A;  4AAZ A;  2N66 A;  1BK8 A;  1JKZ A;  1VNA A;  1JZA A;  1N4N A;  2N69 A;  1FH3 A;  1SEG A;  2LJ7 A;  1B7D A;  2NY8 X; 
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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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#similar chains in the pdb database (?% sequence similarity)
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