5KAFO

Rt xfel structure of photosystem ii in the dark state at 3.0 a resolution
Total Genus 43
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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
43
sequence length
244
structure length
244
Chain Sequence
QTLTYDDIVGTGLANKCPTLDDTARGAYPIDSSQTYRIARLCLQPTTFLVKEEPKNKRQEAEFVPTKLVTRETTSLDQIQGELKVNSDGSLTFVEEDGIDFQPVTVQMAGGERIPLLFTVKNLVASTQPNVTSITTSTDFKGEFNVPSYRTANFLDPKGRGLASGYDSAIALPQAKEEELARANVKRFSLTKGQISLNVAKVDGRTGEIAGTFESEQLSDDDMGAHEPHEVKIQGVFYASIEPA
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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 Structure of photosystem II and substrate binding at room temperature.
pubmed doi rcsb
molecule tags Electron transport
molecule keywords Photosystem II protein D1 1
total genus 43
structure length 244
sequence length 244
chains with identical sequence o
ec nomenclature
pdb deposition date 2016-06-01

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
O PF01716 MSP Manganese-stabilising protein / photosystem II polypeptide
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.160.30 Mainly Beta Beta Barrel Porin Photosystem II, cytochrome c-550 precursor 5kafO01
3.30.2050.10 Alpha Beta 2-Layer Sandwich photosynthetic oxygen evolving center fold photosynthetic oxygen evolving center domain 5kafO02
3A0BO 3KZIO 5E79O 4PJ0O 4UB8O 4IL6O 5GTHO 4UB6O 5H2FO 3JCUO 5G38A 5KAIO 5KAFO 2AXTO 5B5EO 3WU2O 3A0HO 1S5LO 5G39A 5GTIO 5B66O 5TISO 5G3AA
chains in the Genus database with same CATH superfamily
4K3BA 4AKRA 3KZIO 1YS5A 2W81C 5AFUL 5E79O 5GV0A 4KR8A 5ADXK 5D5DA 1T1LA 2K4TA 2R88A 5G26A 4D5UA 2IWWA 2R8AA 4N75A 2LFUA 1GFMA 4C4VB 4BUMX 3PGSA 1ZHXA 3LK3B 4QQ1A 2M07A 3LK2B 3K19A 3WI5A 4E1SA 2ERVA 2N2LA 3SZDA 3VE1A 4AZLA 4B61A 2FGRA 3PF1A 2JMMA 2MHLA 1E54A 2Y0HA 5PRNA 4FZNA 5KAFO 4RJXA 3TZGA 2OMFA 2X9KA 4RJWA 4F4BA 4AUIA 1IZNB 2Y0LA 3PORA 2QTKA 2XMXA 3AAEB 3HOLA 4FSPA 4O3WA 8PRNA 3AA0A 5G39A 2XTQA 3DA4A 4G75A 4GF4A 2KZ7B 5GTIO 2XTRA 5B66O 3QRAA 4O4XA 4GCPA 3LK3A 3BRZA 3POQA 3VZTX 2W80C 3PQUA 4PUXA 5DL6A 4K3CA 1ORMA 1ZHWA 2XE1A 4O3ZA 2F1VA 3VZWX 3AAAB 2N2MA 3JTYA 4KR4A 4O4UA 3SY9A 3AA1B 3EMNX 3PGUA 4G76A 1IZNA 4Z3TA 1MM4A 3QRCA 4AYID 2Y2XA 5H2FO 1QJ8A 2F1TA 2KZ7A 3UPGA 2LHFA 3RBHA 4AYEC 1MM5A 4PR7A 1HXXA 1QJPA 2M06A 4N59A 1HXTA 1T16A 3SY7A 1P4TA 5B5EO 4GCSA 1ZHZA 4FMSA 4AYDC 4FRTA 4AYNA 5IYUA 1ZHYA 1THQA 2YNKA 2KC0A 4LSEA 3SYSA 3UAQA 2MNHA 3PGRA 2X27X 7PRNA 3A0BO 1PHOA 2WVPA 4FRXA 1OPFA 6PRNA 3AAEA 5ADXL 3SZVA 4FQEA 4C69X 2PORA 2R4NA 1QJ9A 3AA0B 4UB8O 3O0EA 1ZHTA 2O4VA 5DL8A 3VY9X 3VY8X 4U9CA 2KDYA 3G7GA 4FSOA 3LK2A 4O49A 4IL6O 3DZMA 2K0LA 3FYXA 3VE2A 1G90A 3GP6A 4UB6O 1H6S1 1PRNA 3A2SX 3NSGA 4KRAA 1BXWA 3KVDD 4C4VA 2ODJA 3AA6A 2XE5A 3BS0A 3HW9A 4AYMC 3JCUO 4FESA 5G38A 5FVNA 2KXPA 4FT6A 3VZUX 4AKRB 2PRNA 2R4LA 3LK42 2AXTO 4FZLA 4CTDA 3AA7B 3LK41 2GE4A 2IWVA 4FUVA 1OSMA 5DL5A 2XE2A 5EE2A 2JQYA 1Q9FA 4FOZA 1Q9GA 5TISO 4C00A 5AFUK 5G3AA 2R4OA 3HOEA 3UU2A 3SYBA 2F1CX 4RL9A 4RLBA 1GFQA 4PJ0O 2J1NA 4AFKA 2ZLDA 3AA6B 2WJRA 4LSIA 2XG6A 3POXA 3T0SA 1GFPA 3DWNA 2J4UP 4AKMA 4LSHA 4D65A 3AA7A 4GHBA 2Y0KA 4O3XB 4GCQA 4JCHA 2YPVA 4JFBA 4N74A 5T5FA 5GTHO 1HXUA 3AA1A 3PRNA 4O3YA 4LSFA 4XNLA 4E1TA 1BT9A 2R4PA 2WJQA 3PQSA 4XNKA 3HWBA 2R89A 2XE3A 3POUA 2FGQX 5KAIO 3BRYA 4FZMA 2Y7SA 1GFOA 3T20A 3DA3A 3C5OA 3V8UA 5DL7A 3WU2O 3WI4A 3NJTA 2ZFGA 3DWOX 4D64A 3A0HO 1S5LO 4N58A 1GFNA 3AAAA 1BH3A 1MPFA 3T24A 4RLCA 2KXPB 5JDPA
chains in the Genus database with same CATH topology
3A0BO 3KZIO 5E79O 4PJ0O 4UB8O 4IL6O 5GTHO 4UB6O 5H2FO 3JCUO 5G38A 5KAIO 5KAFO 2AXTO 5B5EO 3WU2O 3A0HO 1S5LO 5G39A 5GTIO 5B66O 5TISO 5G3AA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3A0B O;  3KZI O;  5E79 O;  4PJ0 O;  4UB8 O;  4IL6 O;  5GTH O;  4UB6 O;  5H2F O;  3JCU O;  5G38 A;  5KAI O;  5KAF O;  2AXT O;  5B5E O;  3WU2 O;  3A0H O;  1S5L O;  5G39 A;  5GTI O;  5B66 O;  5TIS O;  5G3A A; 
#chains in the Genus database with same CATH topology
 4K3B A;  4AKR A;  3KZI O;  1YS5 A;  2W81 C;  5AFU L;  5E79 O;  5GV0 A;  4KR8 A;  5ADX K;  5D5D A;  1T1L A;  2K4T A;  2R88 A;  5G26 A;  4D5U A;  2IWW A;  2R8A A;  4N75 A;  2LFU A;  1GFM A;  4C4V B;  4BUM X;  3PGS A;  1ZHX A;  3LK3 B;  4QQ1 A;  2M07 A;  3LK2 B;  3K19 A;  3WI5 A;  4E1S A;  2ERV A;  2N2L A;  3SZD A;  3VE1 A;  4AZL A;  4B61 A;  2FGR A;  3PF1 A;  2JMM A;  2MHL A;  1E54 A;  2Y0H A;  5PRN A;  4FZN A;  5KAF O;  4RJX A;  3TZG A;  2OMF A;  2X9K A;  4RJW A;  4F4B A;  4AUI A;  1IZN B;  2Y0L A;  3POR A;  2QTK A;  2XMX A;  3AAE B;  3HOL A;  4FSP A;  4O3W A;  8PRN A;  3AA0 A;  5G39 A;  2XTQ A;  3DA4 A;  4G75 A;  4GF4 A;  2KZ7 B;  5GTI O;  2XTR A;  5B66 O;  3QRA A;  4O4X A;  4GCP A;  3LK3 A;  3BRZ A;  3POQ A;  3VZT X;  2W80 C;  3PQU A;  4PUX A;  5DL6 A;  4K3C A;  1ORM A;  1ZHW A;  2XE1 A;  4O3Z A;  2F1V A;  3VZW X;  3AAA B;  2N2M A;  3JTY A;  4KR4 A;  4O4U A;  3SY9 A;  3AA1 B;  3EMN X;  3PGU A;  4G76 A;  1IZN A;  4Z3T A;  1MM4 A;  3QRC A;  4AYI D;  2Y2X A;  5H2F O;  1QJ8 A;  2F1T A;  2KZ7 A;  3UPG A;  2LHF A;  3RBH A;  4AYE C;  1MM5 A;  4PR7 A;  1HXX A;  1QJP A;  2M06 A;  4N59 A;  1HXT A;  1T16 A;  3SY7 A;  1P4T A;  5B5E O;  4GCS A;  1ZHZ A;  4FMS A;  4AYD C;  4FRT A;  4AYN A;  5IYU A;  1ZHY A;  1THQ A;  2YNK A;  2KC0 A;  4LSE A;  3SYS A;  3UAQ A;  2MNH A;  3PGR A;  2X27 X;  7PRN A;  3A0B O;  1PHO A;  2WVP A;  4FRX A;  1OPF A;  6PRN A;  3AAE A;  5ADX L;  3SZV A;  4FQE A;  4C69 X;  2POR A;  2R4N A;  1QJ9 A;  3AA0 B;  4UB8 O;  3O0E A;  1ZHT A;  2O4V A;  5DL8 A;  3VY9 X;  3VY8 X;  4U9C A;  2KDY A;  3G7G A;  4FSO A;  3LK2 A;  4O49 A;  4IL6 O;  3DZM A;  2K0L A;  3FYX A;  3VE2 A;  1G90 A;  3GP6 A;  4UB6 O;  1H6S 1;  1PRN A;  3A2S X;  3NSG A;  4KRA A;  1BXW A;  3KVD D;  4C4V A;  2ODJ A;  3AA6 A;  2XE5 A;  3BS0 A;  3HW9 A;  4AYM C;  3JCU O;  4FES A;  5G38 A;  5FVN A;  2KXP A;  4FT6 A;  3VZU X;  4AKR B;  2PRN A;  2R4L A;  3LK4 2;  2AXT O;  4FZL A;  4CTD A;  3AA7 B;  3LK4 1;  2GE4 A;  2IWV A;  4FUV A;  1OSM A;  5DL5 A;  2XE2 A;  5EE2 A;  2JQY A;  1Q9F A;  4FOZ A;  1Q9G A;  5TIS O;  4C00 A;  5AFU K;  5G3A A;  2R4O A;  3HOE A;  3UU2 A;  3SYB A;  2F1C X;  4RL9 A;  4RLB A;  1GFQ A;  4PJ0 O;  2J1N A;  4AFK A;  2ZLD A;  3AA6 B;  2WJR A;  4LSI A;  2XG6 A;  3POX A;  3T0S A;  1GFP A;  3DWN A;  2J4U P;  4AKM A;  4LSH A;  4D65 A;  3AA7 A;  4GHB A;  2Y0K A;  4O3X B;  4GCQ A;  4JCH A;  2YPV A;  4JFB A;  4N74 A;  5T5F A;  5GTH O;  1HXU A;  3AA1 A;  3PRN A;  4O3Y A;  4LSF A;  4XNL A;  4E1T A;  1BT9 A;  2R4P A;  2WJQ A;  3PQS A;  4XNK A;  3HWB A;  2R89 A;  2XE3 A;  3POU A;  2FGQ X;  5KAI O;  3BRY A;  4FZM A;  2Y7S A;  1GFO A;  3T20 A;  3DA3 A;  3C5O A;  3V8U A;  5DL7 A;  3WU2 O;  3WI4 A;  3NJT A;  2ZFG A;  3DWO X;  4D64 A;  3A0H O;  1S5L O;  4N58 A;  1GFN A;  3AAA A;  1BH3 A;  1MPF A;  3T24 A;  4RLC A;  2KXP B;  5JDP A; 
#chains in the Genus database with same CATH homology
 3A0B O;  3KZI O;  5E79 O;  4PJ0 O;  4UB8 O;  4IL6 O;  5GTH O;  4UB6 O;  5H2F O;  3JCU O;  5G38 A;  5KAI O;  5KAF O;  2AXT O;  5B5E O;  3WU2 O;  3A0H O;  1S5L O;  5G39 A;  5GTI O;  5B66 O;  5TIS O;  5G3A A; 
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similar chains in the pdb database (?% sequence similarity)

 
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