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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molecule keywords Photosystem II protein D1 1
publication title Structure of photosystem II and substrate binding at room temperature.
pubmed doi rcsb
molecule tags Electron transport
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
2AXTO 5GTIO 4PJ0O 3A0BO 4UB8O 3WU2O 5H2FO 5KAFO 5B5EO 5G39A 3JCUO 1S5LO 3A0HO 4IL6O 5TISO 4UB6O 5KAIO 3KZIO 5G3AA 5B66O 5E79O 5G38A 5GTHO
chains in the Genus database with same CATH superfamily
1HXXA 1IZNA 1MM5A 2AXTO 3DA4A 3DWNA 4PJ0O 3A0BO 5ADXK 2KC0A 2WJQA 5H2FO 4AYID 2JQYA 4O4XA 1T1LA 4RJWA 6PRNA 4N58A 2Y0KA 3VE2A 3AAEA 3PGRA 3UU2A 4FQEA 4N75A 3GP6A 4E1TA 3BRYA 4K3BA 4QQ1A 3PF1A 2XE2A 3LK2A 3A0HO 3AA0B 4KR4A 1T16A 1P4TA 2LFUA 4N59A 4D64A 4D65A 8PRNA 2XE5A 4GCSA 3SYSA 3UPGA 2YNKA 3LK3A 5EE2A 2KXPB 4LSFA 4FZLA 3VY9X 4AYMC 2KZ7B 4B61A 1H6S1 2GE4A 5GTHO 4O3WA 1ZHXA 3G7GA 3O0EA 4D5UA 5GTIO 1BT9A 1QJ9A 4KR8A 4C69X 3AA1B 4UB8O 1ZHYA 4O3XB 4AYDC 2IWVA 2PRNA 2XTQA 4FZMA 1OSMA 2OMFA 7PRNA 4AKRA 5B5EO 3AA6B 4FUVA 4GCQA 4C4VB 3SZDA 3HW9A 3JCUO 4FSPA 3WI4A 4AZLA 2Y2XA 5ADXL 4LSIA 3POQA 1THQA 3T0SA 3NSGA 3VZWX 2K0LA 1OPFA 2X27X 2KDYA 1MPFA 4GCPA 3VY8X 3QRAA 1BXWA 3K19A 3AA1A 5TISO 3V8UA 1GFMA 2R4OA 4Z3TA 2YPVA 4N74A 3FYXA 3HWBA 4G76A 4FZNA 2Y0HA 3AA6A 2F1TA 2K4TA 3KZIO 3PGSA 3PRNA 2ZLDA 4FMSA 4PUXA 2F1VA 3DZMA 5G26A 5G3AA 4C4VA 1Q9GA 3PQUA 5B66O 4F4BA 3VZTX 4O49A 4C00A 4BUMX 4FT6A 3AA7B 1PHOA 3EMNX 2R88A 4O3ZA 1GFNA 3AA0A 3DWOX 2XTRA 3SY7A 5T5FA 2PORA 3VZUX 2N2LA 5JDPA 2IWWA 5G39A 2R4PA 2LHFA 2WVPA 4G75A 2WJRA 3HOLA 4K3CA 5IYUA 3PORA 5PRNA 1HXUA 1IZNB 2KXPA 1S5LO 2KZ7A 1GFQA 2XG6A 3POXA 3QRCA 5DL6A 2QTKA 5D5DA 4AYNA 2W80C 3DA3A 4GF4A 4AUIA 2O4VA 1BH3A 4JFBA 4KRAA 3AAAB 4PR7A 3BRZA 4RL9A 3PQSA 3JTYA 4U9CA 3AAEB 4FRXA 3SY9A 5FVNA 2R89A 3PGUA 4FESA 4UB6O 4FOZA 4LSHA 1GFOA 5KAIO 3SYBA 3LK2B 2R4NA 2XMXA 3A2SX 3C5OA 1E54A 5E79O 1QJPA 1ZHZA 4RLBA 5DL5A 5G38A 3RBHA 1ORMA 3UAQA 5AFUK 2J4UP 1YS5A 2R4LA 4O4UA 5DL8A 2M06A 2N2MA 2ZFGA 2ERVA 1MM4A 1QJ8A 3KVDD 3LK3B 4RLCA 3WU2O 3AAAA 3NJTA 4GHBA 5KAFO 3VE1A 5AFUL 5DL7A 4FSOA 1PRNA 2J1NA 2XE3A 2Y0LA 4XNKA 4E1SA 2MNHA 1HXTA 3T24A 4JCHA 2X9KA 2Y7SA 3LK41 4FRTA 3WI5A 1ZHTA 4IL6O 4AKRB 1G90A 4AYEC 3BS0A 4CTDA 3POUA 4O3YA 2ODJA 3T20A 3AA7A 2W81C 5GV0A 4LSEA 2JMMA 3HOEA 1Q9FA 4XNLA 3SZVA 1ZHWA 1GFPA 4AKMA 2XE1A 2FGQX 4AFKA 2MHLA 2F1CX 2FGRA 2M07A 4RJXA 3LK42 3TZGA 2R8AA
chains in the Genus database with same CATH topology
2AXTO 5GTIO 4PJ0O 3A0BO 4UB8O 3WU2O 5H2FO 5KAFO 5B5EO 5G39A 3JCUO 1S5LO 3A0HO 4IL6O 5TISO 4UB6O 5KAIO 3KZIO 5G3AA 5B66O 5E79O 5G38A 5GTHO
chains in the Genus database with same CATH homology


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

 
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