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


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