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


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