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


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