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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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
molecule tags Immune system/toxin
source organism Homo sapiens
molecule keywords SINGLE CHAIN ANTIBODY FRAGMENT 9004G
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
1JZBA 4HE7A 1L4VA 1SN4A 1JKZA 2N69A 1OMYA 2NY8X 1SN1A 1WWNA 3PSMA 1I6FA 2LJMA 1WT7A 1NRAA 2B3CA 2SN3A 2KSKA 1ZFUA 1I6GA 1LQHA 1VNAA 1VNBA 1GPTA 2LKBA 3E7RL 2KPYA 2B68A 1PX9A 1ZUTA 1NH5A 1ZYVA 1OZZA 2YEOA 1NPIA 2KBKA 1NRBA 1T0ZA 2E3FA 1I2UA 4AEIA 2KYQA 2KJAA 1KV0A 1SNBA 1BCGA 2LR3A 2LI7A 1B3CA 1TI5A 4AB0A 1C56A 1T7BA 1MR4A 1P0AA 2LJ7A 4CQKA 1JXCA 1P00A 2LY6A 2MZ0A 2YC1C 1BRZA 2M8BB 1T7EA 1SEGA 5KK4A 1ICAA 2N2RA 4HHFA 1C55A 2NY9X 1LQQA 1GPSA 2YBRC 1AYJA 2A7TA 2KBJA 1WMTA 2N66A 1T1TA 4KYPA 2KGQA 1DJTA 2LY5A 1LQIA 1I2VA 2E0HA 1ZVGA 1MYNA 2BRZA 1ZU3A 4AAZA 1JZAA 2E3GA 1DQ7A 1ZYWA 2I61A 4UJ0A 2LT8A 2ASCA 5CY0A 2KBHA 1PTXA 1NE5A 1B7DA 1PE4A 2GL1A 1BMRA 2N2QA 1N4NA 1FH3A 1CHZA 4V1DC 3E7UX 1AHOA 1ZVEA 1T7AA 2ATBA 1CN2A 1BK8A
chains in the Genus database with same CATH superfamily
2YIPA 1JZBA 4HE7A 1NGEA 5AQSA 1L4VA 5AQXA 1SN4A 1JKZA 2N69A 5AQTA 2E8AA 1OMYA 5BPLA 2QWPA 2KHOA 4H5NA 2NY8X 1SN1A 1NGIA 5FPNA 1WWNA 1QQMA 4H5WA 3PSMA 1I6FA 2LJMA 1NGAA 3KC6A 1WT7A 3QFUA 1NRAA 4KBOA 5AQWA 1QQNA 2B3CA 3KP1A 3QMLA 2SN3A 3ATVA 3GKUA 5F0XA 2KSKA 1ZFUA 2JDQD 3CQXA 1KAZA 1I6GA 1LQHA 4H5VA 2QWRA 1VNAA 5AQYA 1VNBA 1ATSA 5BN9A 1DKGD 3FZKA 1GPTA 2LKBA 3E7RL 3IUCA 2KPYA 1KAXA 3LDOA 3KHWA 2B68A 1PX9A 3KVGA 4GNIA 3SF4D 1POIA 5AQNA 3LDLA 5F2RA 5AQRA 1ZUTA 2QWOA 4H5RA 1HX1A 1KAYA 3FE1A 3I33A 1NGDA 5AQGA 5AQLA 1NH5A 1BA0A 2QXLA 1ZYVA 1OZZA 4UAFE 2YEOA 2BUPA 2LN8A 5AQIA 1NPIA 2KBKA 5AQKA 5AQZA 1NRBA 1QQOA 1BA1A 1T0ZA 2E3FA 4H5TA 5BN8A 5AQFA 1I2UA 4AEIA 1NGFA 2KYQA 3C7NB 5F1XA 2KJAA 1KV0A 3QFPA 5EX5A 3AY9A 1AYJA 1SNBA 2QWQA 3C7NA 5EY4A 1BCGA 3LDNA 2LR3A 2LI7A 3FZMA 5AQOA 3L56A 3ATUA 3LDQA 1YUWA 1B3CA 1K8BA 3QI7A 1TI5A 1XRSB 2QW9A 4AB0A 1C56A 1T7BA 1MR4A 1P0AA 3JXUA 2GMOA 2LJ7A 3D2EB 3FZFA 2QWMA 5FPEA 4UAEF 2MBKA 2QWLA 3GL1A 4CQKA 4UADE 1S3XA 1JXCA 1P00A 4IO8A 3R2VA 1NGJA 2YIOA 1HJOA 2LY6A 3A8YA 2K35A 2MZ0A 3D2EA 1NGCA 2YC1C 1BRZA 2M8BB 3FZHA 1T7EA 3CW4A 1SEGA 3KOYA 3BK3C 3L4IA 5KK4A 3FZLA 1ICAA 2N2RA 3D2FB 2VY6A 3LDPA 4HHFA 1C55A 2MN5A 3KP0A 2NY9X 1LQQA 1GPSA 1NGHA 3KOXA 2YBRC 3GDQA 2A7TA 2V7ZA 4FSVA 3D2FA 4HWIA 2KBJA 5AQPA 5EVZA 1HPMA 2D56A 1WMTA 2N66A 1T1TA 4KYPA 2KGQA 1DJTA 2LY5A 1LQIA 1I2VA 2E0HA 3KOWA 1ZVGA 1MYNA 2BRZA 2E2FA 1ZU3A 3KOZA 5AQHA 5BPNA 4AAZA 5BPMA 5AR0A 3L6QA 1ATRA 1JZAA 1UGLA 3M3ZA 2E3GA 5AQMA 1DQ7A 3HSCA 1ZYWA 2I61A 1BUPA 5AQJA 4UJ0A 1NGGA 2LT8A 2QWNA 5AQQA 5AQVA 2YILA 2ASCA 5CY0A 2KBHA 1PTXA 1NE5A 1B7DA 1PE4A 2GL1A 1BMRA 5FPMA 2N2QA 4FL9A 5AQUA 1N4NA 1FH3A 1CHZA 4V1DC 5EXWA 3E7UX 1AHOA 1ZVEA 2E88A 2G2KA 5FPDA 1T7AA 1NGBA 2ATBA 1CN2A 1BK8A
chains in the Genus database with same CATH topology
1JZBA 4HE7A 1L4VA 1SN4A 1JKZA 2N69A 1OMYA 2NY8X 1SN1A 1WWNA 3PSMA 1I6FA 2LJMA 1WT7A 1NRAA 2B3CA 2SN3A 2KSKA 1ZFUA 1I6GA 1LQHA 1VNAA 1VNBA 1GPTA 2LKBA 3E7RL 2KPYA 2B68A 1PX9A 1ZUTA 1NH5A 1ZYVA 1OZZA 2YEOA 1NPIA 2KBKA 1NRBA 1T0ZA 2E3FA 1I2UA 4AEIA 2KYQA 2KJAA 1KV0A 1SNBA 1BCGA 2LR3A 2LI7A 1B3CA 1TI5A 4AB0A 1C56A 1T7BA 1MR4A 1P0AA 2LJ7A 4CQKA 1JXCA 1P00A 2LY6A 2MZ0A 2YC1C 1BRZA 2M8BB 1T7EA 1SEGA 5KK4A 1ICAA 2N2RA 4HHFA 1C55A 2NY9X 1LQQA 1GPSA 2YBRC 1AYJA 2A7TA 2KBJA 1WMTA 2N66A 1T1TA 4KYPA 2KGQA 1DJTA 2LY5A 1LQIA 1I2VA 2E0HA 1ZVGA 1MYNA 2BRZA 1ZU3A 4AAZA 1JZAA 2E3GA 1DQ7A 1ZYWA 2I61A 4UJ0A 2LT8A 2ASCA 5CY0A 2KBHA 1PTXA 1NE5A 1B7DA 1PE4A 2GL1A 1BMRA 2N2QA 1N4NA 1FH3A 1CHZA 4V1DC 3E7UX 1AHOA 1ZVEA 1T7AA 2ATBA 1CN2A 1BK8A
chains in the Genus database with same CATH homology


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