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


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

 
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