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


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

 
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