5KK4A

Crystal structure of the plant defensin nsd7 bound to phosphatidic acid
Total Genus 12
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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
12
sequence length
47
structure length
47
Chain Sequence
KDCKRESNTFPGICITKPPCRKACIREKFTDGHCSKILRRCLCTKPC
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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 NsD7
publication title Binding of phosphatidic acid by NsD7 mediates the formation of helical defensin-lipid oligomeric assemblies and membrane permeabilization.
pubmed doi rcsb
source organism Nicotiana suaveolens x nicotiana tabacum
molecule tags Antimicrobial protein
total genus 12
structure length 47
sequence length 47
chains with identical sequence B, C, D, E, F
ec nomenclature
pdb deposition date 2016-06-21

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00304 Gamma-thionin Gamma-thionin family
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 5kk4A00
1JZAA 2I61A 2NY9X 2ATBA 2N66A 1DQ7A 1SEGA 4UJ0A 1MYNA 1LQHA 1N4NA 1L4VA 2N2QA 2N2RA 5KK4A 2KJAA 2E3FA 1I6FA 1WWNA 2KGQA 2E3GA 1ICAA 1LQQA 1NPIA 2M8BB 1PX9A 1NRAA 1I2VA 1OZZA 1OMYA 2YEOA 4AEIA 2KBKA 2LR3A 2E0HA 1B7DA 1CHZA 1LQIA 1ZYWA 2B68A 1PE4A 1C55A 1AHOA 3E7RL 4AB0A 2KBJA 4HHFA 1WMTA 3PSMA 5CY0A 3E7UX 1ZVEA 2GL1A 4KYPA 2YC1C 1JKZA 1BRZA 1FH3A 2LY5A 1I6GA 1T1TA 1SN4A 2LJ7A 2KPYA 1CN2A 2LI7A 1AYJA 1PTXA 4CQKA 2N69A 1P00A 1WT7A 1KV0A 4HE7A 2NY8X 2LKBA 1B3CA 2SN3A 2KYQA 4AAZA 1T0ZA 1MR4A 2LT8A 2MZ0A 1VNBA 1NRBA 1T7AA 2LY6A 1NE5A 1ZFUA 1BCGA 1GPSA 2KSKA 1BK8A 1JZBA 1I2UA 1VNAA 2KBHA 1ZYVA 1P0AA 2B3CA 1C56A 2A7TA 1ZU3A 2BRZA 1DJTA 4V1DC 1SN1A 2ASCA 1ZUTA 1GPTA 1ZVGA 1NH5A 2LJMA 1JXCA 1T7BA 1T7EA 1BMRA 1TI5A 2YBRC 1SNBA
chains in the Genus database with same CATH superfamily
2QWLA 1HX1A 1JZAA 5BPNA 1KAXA 2I61A 2NY9X 2ATBA 2N66A 1DQ7A 3L4IA 4UAFE 1QQNA 1SEGA 4UJ0A 1MYNA 1LQHA 2LN8A 2QWNA 3FZKA 1UGLA 1N4NA 3GKUA 1QQMA 5FPEA 5AQUA 2N2QA 1KAZA 1L4VA 3QMLA 2N2RA 5KK4A 1DKGD 2KJAA 2E3FA 5BPLA 1I6FA 1WWNA 2KGQA 2MBKA 3A8YA 2E3GA 3SF4D 1ICAA 3C7NB 1HPMA 1LQQA 1NGAA 3KHWA 3FZHA 3LDOA 1NPIA 2M8BB 2QWPA 5BN8A 1PX9A 1NRAA 1I2VA 1OZZA 3R2VA 1OMYA 2YEOA 4AEIA 5FPDA 2KBKA 2LR3A 5F2RA 3JXUA 2E0HA 3FZMA 1NGCA 2QW9A 4UADE 3ATVA 3L6QA 5F1XA 1NGGA 5AQTA 1B7DA 5AQHA 1CHZA 5AQOA 1LQIA 1ZYWA 2B68A 1PE4A 5AQWA 4FSVA 3BK3C 1C55A 1AHOA 3C7NA 5AQPA 2JDQD 5AR0A 3QFPA 3LDQA 1S3XA 3E7RL 3KOZA 4AB0A 2KBJA 4H5VA 1WMTA 3PSMA 4HHFA 5CY0A 3E7UX 1ZVEA 2GL1A 4KYPA 2G2KA 2YC1C 1JKZA 1BRZA 1FH3A 2GMOA 2KHOA 2LY5A 2QWOA 1I6GA 5AQMA 1T1TA 1NGHA 2MN5A 1BA0A 1SN4A 2LJ7A 2KPYA 1NGFA 1XRSB 2QWMA 3D2EA 4H5WA 5AQLA 5AQFA 3GL1A 2YIOA 5AQQA 5EY4A 1CN2A 2LI7A 4HWIA 5AQRA 1NGBA 3HSCA 2E2FA 1AYJA 1PTXA 3KOWA 5AQNA 1NGIA 4CQKA 3D2EB 3I33A 1NGDA 2QXLA 2N69A 1P00A 1WT7A 1KV0A 2E88A 2NY8X 3D2FB 3FZLA 4H5NA 1ATSA 2LKBA 3KVGA 4HE7A 4UAEF 1B3CA 2YILA 2SN3A 2KYQA 3KOXA 4AAZA 3KC6A 2BUPA 5AQJA 1T0ZA 5AQIA 3QI7A 3IUCA 3QFUA 1MR4A 2QWRA 4KBOA 2LT8A 2MZ0A 5FPMA 1VNBA 3LDPA 5AQXA 2QWQA 3AY9A 5FPNA 1NRBA 1T7AA 2LY6A 5BN9A 3FE1A 3KP1A 1NE5A 4GNIA 1NGEA 2D56A 3L56A 4IO8A 1ZFUA 1BCGA 1HJOA 3GDQA 1YUWA 3D2FA 3ATUA 4H5RA 3FZFA 5AQGA 1GPSA 2KSKA 1BK8A 1JZBA 5AQYA 1ATRA 1QQOA 1I2UA 1VNAA 2KBHA 1NGJA 1P0AA 1ZYVA 2B3CA 1C56A 5AQSA 5EXWA 2A7TA 1ZU3A 3CW4A 2BRZA 1DJTA 5F0XA 5AQZA 4V1DC 3LDNA 4FL9A 2K35A 3CQXA 1SN1A 2VY6A 5AQKA 2ASCA 1K8BA 1ZUTA 1GPTA 3KP0A 3M3ZA 3KOYA 1ZVGA 5EX5A 1NH5A 5EVZA 5BPMA 2LJMA 1JXCA 2YIPA 1T7BA 2E8AA 1BUPA 1KAYA 1T7EA 1TI5A 3LDLA 5AQVA 1BMRA 2YBRC 1SNBA 1BA1A 1POIA 4H5TA 2V7ZA
chains in the Genus database with same CATH topology
1JZAA 2I61A 2NY9X 2ATBA 2N66A 1DQ7A 1SEGA 4UJ0A 1MYNA 1LQHA 1N4NA 1L4VA 2N2QA 2N2RA 5KK4A 2KJAA 2E3FA 1I6FA 1WWNA 2KGQA 2E3GA 1ICAA 1LQQA 1NPIA 2M8BB 1PX9A 1NRAA 1I2VA 1OZZA 1OMYA 2YEOA 4AEIA 2KBKA 2LR3A 2E0HA 1B7DA 1CHZA 1LQIA 1ZYWA 2B68A 1PE4A 1C55A 1AHOA 3E7RL 4AB0A 2KBJA 4HHFA 1WMTA 3PSMA 5CY0A 3E7UX 1ZVEA 2GL1A 4KYPA 2YC1C 1JKZA 1BRZA 1FH3A 2LY5A 1I6GA 1T1TA 1SN4A 2LJ7A 2KPYA 1CN2A 2LI7A 1AYJA 1PTXA 4CQKA 2N69A 1P00A 1WT7A 1KV0A 4HE7A 2NY8X 2LKBA 1B3CA 2SN3A 2KYQA 4AAZA 1T0ZA 1MR4A 2LT8A 2MZ0A 1VNBA 1NRBA 1T7AA 2LY6A 1NE5A 1ZFUA 1BCGA 1GPSA 2KSKA 1BK8A 1JZBA 1I2UA 1VNAA 2KBHA 1ZYVA 1P0AA 2B3CA 1C56A 2A7TA 1ZU3A 2BRZA 1DJTA 4V1DC 1SN1A 2ASCA 1ZUTA 1GPTA 1ZVGA 1NH5A 2LJMA 1JXCA 1T7BA 1T7EA 1BMRA 1TI5A 2YBRC 1SNBA
chains in the Genus database with same CATH homology


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