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


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