5KK4A

Crystal structure of the plant defensin nsd7 bound to phosphatidic acid
Total Genus 12

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

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
EMPTYS1 (2-6)S3 (41-46)TI1 (7-10)TIV2 (36-39)S2 (31-34)AH1 (17-27)TIV1 (35-38)Updating...
connected with : NaN
molecule tags Antimicrobial protein
source organism Nicotiana suaveolens x nicotiana tabacum
publication title Binding of phosphatidic acid by NsD7 mediates the formation of helical defensin-lipid oligomeric assemblies and membrane permeabilization.
pubmed doi rcsb
molecule keywords NsD7
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
1ZVEA 2LR3A 2GL1A 4UJ0A 1NRBA 2KBKA 1B7DA 1T7EA 1DQ7A 2N2QA 1I2UA 2KPYA 2LI7A 1BCGA 1ZUTA 2LY5A 2LJ7A 1I2VA 1JZAA 1C55A 1KV0A 2ATBA 2BRZA 1DJTA 1WT7A 1SEGA 1MR4A 4AEIA 1WWNA 2KSKA 2ASCA 2E3FA 5CY0A 1CN2A 1BMRA 2E3GA 4CQKA 1OMYA 2I61A 2KYQA 1PX9A 1AHOA 1T0ZA 1NH5A 2E0HA 4HE7A 1I6FA 2A7TA 1MYNA 4HHFA 3E7UX 1CHZA 4AB0A 2B68A 2YEOA 1ZYVA 1VNAA 1ZYWA 2LJMA 2SN3A 4KYPA 1I6GA 1ZU3A 1SNBA 1JKZA 1OZZA 1T7AA 2N69A 1N4NA 1VNBA 1TI5A 1GPSA 2M8BB 1WMTA 1AYJA 3E7RL 2MZ0A 2KBJA 1ICAA 1L4VA 2LY6A 1NPIA 1P00A 2YC1C 2B3CA 1BRZA 2YBRC 1PE4A 1T1TA 1BK8A 1C56A 1PTXA 1SN4A 2KBHA 1ZVGA 1GPTA 4AAZA 1LQIA 2N66A 1T7BA 1P0AA 2N2RA 2NY8X 2KGQA 2KJAA 1NE5A 1NRAA 1SN1A 1JZBA 2NY9X 3PSMA 1LQQA 1FH3A 1JXCA 1LQHA 1ZFUA 4V1DC 1B3CA 2LT8A 5KK4A 2LKBA
chains in the Genus database with same CATH superfamily
1ZVEA 2LR3A 2GL1A 3LDQA 2YILA 3FZFA 3IUCA 4UJ0A 1NRBA 3C7NB 2GMOA 5FPDA 2KBKA 4FSVA 1B7DA 3C7NA 3GDQA 1T7EA 1DQ7A 2N2QA 3FZMA 3R2VA 1HJOA 1QQOA 1I2UA 5AQKA 1DKGD 2KPYA 2LI7A 5F0XA 1BCGA 2QWMA 1ZUTA 2LY5A 1NGCA 2LJ7A 1UGLA 1I2VA 3KVGA 3KOZA 1JZAA 2QWNA 3CW4A 4H5WA 5AQWA 1KV0A 1C55A 3L6QA 2LN8A 2ATBA 1KAZA 2BRZA 1XRSB 2E88A 3CQXA 3D2FB 1ATSA 1DJTA 1WT7A 3QMLA 3JXUA 1SEGA 1MR4A 3D2FA 5AQRA 2QWLA 1NGFA 1WWNA 3KC6A 3KOWA 4AEIA 4H5VA 3FE1A 2KSKA 2ASCA 3LDLA 2E3FA 2K35A 3SF4D 5CY0A 1CN2A 2QWRA 1ATRA 3D2EB 3ATUA 1QQMA 3L56A 4HWIA 5AQGA 1QQNA 2E3GA 4CQKA 1BMRA 3D2EA 1NGJA 5F2RA 1OMYA 2I61A 5BN8A 5AR0A 2KYQA 5AQVA 1PX9A 1AHOA 3L4IA 3A8YA 5AQXA 1T0ZA 5FPMA 5AQPA 4GNIA 4UADE 5AQHA 1NH5A 2E0HA 4HE7A 5AQZA 1I6FA 3QFUA 5AQOA 2JDQD 5AQIA 3KHWA 2A7TA 5EY4A 1MYNA 3KP1A 3GL1A 1NGDA 3E7UX 1CHZA 1NGAA 2G2KA 3KOYA 4HHFA 4AB0A 5BPMA 1NGGA 2B68A 5EX5A 2MBKA 2YEOA 1ZYVA 2MN5A 3LDPA 4H5TA 1VNAA 1BA1A 1KAYA 1ZYWA 2E8AA 1HX1A 2BUPA 2LJMA 2SN3A 1ZU3A 4KYPA 1SNBA 5AQMA 5AQUA 1JKZA 5AQQA 3M3ZA 3FZKA 5EVZA 1OZZA 1T7AA 2N69A 1N4NA 5BPLA 4UAEF 3ATVA 1VNBA 5AQJA 2QXLA 1TI5A 1HPMA 1GPSA 2M8BB 5EXWA 1KAXA 1WMTA 1AYJA 3HSCA 3E7RL 4UAFE 5AQTA 2MZ0A 2KBJA 1ICAA 2YIOA 3I33A 2VY6A 2YIPA 1L4VA 2LY6A 1NPIA 5FPEA 1P00A 2YC1C 2B3CA 5F1XA 1NGEA 1BRZA 2QWOA 2YBRC 1PE4A 1NGHA 1T1TA 5BPNA 1BK8A 3KP0A 1C56A 1PTXA 3FZLA 5AQLA 1SN4A 2KBHA 1ZVGA 5FPNA 1GPTA 5AQFA 1S3XA 1YUWA 3KOXA 4AAZA 1LQIA 1POIA 2N66A 4FL9A 1T7BA 1P0AA 2N2RA 4IO8A 5AQYA 5BN9A 1NGIA 3QI7A 3QFPA 2NY8X 2KGQA 2KJAA 2D56A 1NE5A 1NRAA 4KBOA 2V7ZA 1BUPA 3FZHA 1I6GA 2E2FA 2QWQA 3BK3C 4H5NA 4H5RA 1SN1A 1JZBA 2QWPA 2NY9X 3PSMA 2QW9A 1LQQA 5AQNA 3GKUA 3LDNA 1FH3A 1JXCA 1LQHA 1ZFUA 1NGBA 4V1DC 1B3CA 3AY9A 2LT8A 2KHOA 3LDOA 5KK4A 5AQSA 2LKBA 1K8BA 1BA0A
chains in the Genus database with same CATH topology
1ZVEA 2LR3A 2GL1A 4UJ0A 1NRBA 2KBKA 1B7DA 1T7EA 1DQ7A 2N2QA 1I2UA 2KPYA 2LI7A 1BCGA 1ZUTA 2LY5A 2LJ7A 1I2VA 1JZAA 1C55A 1KV0A 2ATBA 2BRZA 1DJTA 1WT7A 1SEGA 1MR4A 4AEIA 1WWNA 2KSKA 2ASCA 2E3FA 5CY0A 1CN2A 1BMRA 2E3GA 4CQKA 1OMYA 2I61A 2KYQA 1PX9A 1AHOA 1T0ZA 1NH5A 2E0HA 4HE7A 1I6FA 2A7TA 1MYNA 4HHFA 3E7UX 1CHZA 4AB0A 2B68A 2YEOA 1ZYVA 1VNAA 1ZYWA 2LJMA 2SN3A 4KYPA 1I6GA 1ZU3A 1SNBA 1JKZA 1OZZA 1T7AA 2N69A 1N4NA 1VNBA 1TI5A 1GPSA 2M8BB 1WMTA 1AYJA 3E7RL 2MZ0A 2KBJA 1ICAA 1L4VA 2LY6A 1NPIA 1P00A 2YC1C 2B3CA 1BRZA 2YBRC 1PE4A 1T1TA 1BK8A 1C56A 1PTXA 1SN4A 2KBHA 1ZVGA 1GPTA 4AAZA 1LQIA 2N66A 1T7BA 1P0AA 2N2RA 2NY8X 2KGQA 2KJAA 1NE5A 1NRAA 1SN1A 1JZBA 2NY9X 3PSMA 1LQQA 1FH3A 1JXCA 1LQHA 1ZFUA 4V1DC 1B3CA 2LT8A 5KK4A 2LKBA
chains in the Genus database with same CATH homology


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