5GTHO

Native xfel structure of photosystem ii (dark dataset)
Total Genus 52
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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
52
sequence length
243
structure length
243
Chain Sequence
b'TLTYDDIVGTGLANKCPTLDDTARGAYPIDSSQTYRIARLCLQPTTFLVKEEPKNKRQEAEFVPTKLVTRETTSLDQIQGELKVNSDGSLTFVEEDGIDFQPVTVQMAGGERIPLLFTVKNLVASTQPNVTSITTSTDFKGEFNVPSYRTANFLDPKGRGLASGYDSAIALPQAKEEELARANVKRFSLTKGQISLNVAKVDGRTGEIAGTFESEQLSDDDMGAHEPHEVKIQGVFYASIEPA'
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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
publication title Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.
pubmed doi rcsb
molecule tags Photosynthesis
total genus 52
structure length 243
sequence length 243
chains with identical sequence o
ec nomenclature
pdb deposition date 2016-08-20

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 5gthO01
3.30.2050.10 Alpha Beta 2-Layer Sandwich photosynthetic oxygen evolving center fold photosynthetic oxygen evolving center domain 5gthO02
3KZIO 1S5LO 5H2FO 5B66O 2AXTO 3A0BO 5KAFO 4IL6O 5G3AA 5TISO 5KAIO 5GTIO 5G39A 3A0HO 3JCUO 5B5EO 5E79O 5GTHO 3WU2O 4UB6O 5G38A 4UB8O 4PJ0O
chains in the Genus database with same CATH superfamily
2J1NA 4FRTA 5G26A 3POUA 3QRCA 3SYSA 1ZHWA 4AZLA 8PRNA 2J4UP 4AYDC 4FZMA 2M07A 1ZHXA 2Y7SA 3HOEA 1QJPA 3K19A 3PRNA 5KAFO 3AAEB 4K3BA 1IZNA 2F1TA 4N58A 2XE3A 3VZWX 5G3AA 5TISO 5KAIO 1ZHTA 3DWOX 3PF1A 4AKRA 1BXWA 4AYMC 3JCUO 4PR7A 4KRAA 4FUVA 1QJ9A 2K0LA 3BRZA 4JCHA 2JMMA 2ZLDA 2KC0A 1H6S1 2W81C 4RJWA 4RLBA 3LK3B 4LSEA 2YPVA 2IWWA 2KXPA 4FZNA 4XNKA 4C4VA 1GFOA 1HXUA 3PGRA 3LK42 4D5UA 3V8UA 2KZ7A 4XNLA 3VE2A 4C00A 1MPFA 4GHBA 4FQEA 5DL7A 4AYNA 4C69X 4G76A 4N75A 5DL8A 2MHLA 2MNHA 3NJTA 4AKMA 1ZHZA 2FGRA 2X27X 2XG6A 2X9KA 3PORA 5DL6A 3LK2A 2PORA 3G7GA 2XTRA 2AXTO 2LHFA 3A0BO 4FMSA 3AAEA 4IL6O 1PRNA 4N59A 4PUXA 3A2SX 2R4LA 3SZVA 2WJQA 3RBHA 2XE2A 3UU2A 3VY9X 3UPGA 3DWNA 5GTIO 2R8AA 2XTQA 3BRYA 3WI4A 1MM5A 1E54A 3AA6A 4O4UA 5FVNA 2FGQX 5AFUL 2PRNA 2R4OA 3LK3A 4FT6A 3WI5A 3WU2O 4GCQA 3PQSA 4O3ZA 4UB6O 4Z3TA 2R4PA 1MM4A 2LFUA 3JTYA 1BH3A 2JQYA 3PQUA 4O4XA 4CTDA 4FESA 4G75A 2QTKA 4GCPA 1GFQA 2KDYA 2XMXA 1OSMA 6PRNA 2IWVA 4PJ0O 4FOZA 4LSFA 1GFNA 5DL5A 3T20A 2F1VA 2WVPA 1S5LO 4O49A 3VE1A 2Y2XA 3AAAB 3KVDD 3SY9A 3NSGA 5IYUA 2N2MA 5H2FO 3PGSA 4N74A 4B61A 2ERVA 2Y0LA 4O3YA 4GCSA 4LSIA 5G39A 5PRNA 3SYBA 1T1LA 4O3WA 3SZDA 1P4TA 3O0EA 4AFKA 4RLCA 3HWBA 3VZUX 4RJXA 1QJ8A 2R88A 1GFPA 2XE1A 5GV0A 2W80C 3SY7A 3AA1B 3DA3A 3AA7B 3C5OA 1HXXA 7PRNA 4K3CA 2N2LA 5ADXL 4D65A 1T16A 2O4VA 4KR8A 1OPFA 1G90A 1ZHYA 4AYEC 3DZMA 4UB8O 2M06A 3AA0B 1Q9FA 2ODJA 3KZIO 3GP6A 4FSOA 4F4BA 3BS0A 4FZLA 3POXA 3T24A 2F1CX 3AAAA 3LK2B 4FRXA 4GF4A 4BUMX 2WJRA 5B66O 4JFBA 3UAQA 3TZGA 2OMFA 4O3XB 5JDPA 5D5DA 4U9CA 4QQ1A 5AFUK 2XE5A 2R4NA 1IZNB 1BT9A 1THQA 1YS5A 2Y0KA 3PGUA 3POQA 3QRAA 4AYID 4AKRB 3AA6B 4FSPA 2GE4A 3A0HO 3LK41 5EE2A 1GFMA 3VY8X 3VZTX 4E1TA 5T5FA 3T0SA 5B5EO 4E1SA 5E79O 4D64A 5GTHO 3FYXA 1ORMA 2Y0HA 4RL9A 1PHOA 2KXPB 3DA4A 2ZFGA 3AA1A 5G38A 4C4VB 3HW9A 5ADXK 1Q9GA 3AA7A 4AUIA 2R89A 2K4TA 3HOLA 2KZ7B 3EMNX 4LSHA 2YNKA 1HXTA 4KR4A 3AA0A
chains in the Genus database with same CATH topology
3KZIO 1S5LO 5H2FO 5B66O 2AXTO 3A0BO 5KAFO 4IL6O 5G3AA 5TISO 5KAIO 5GTIO 5G39A 3A0HO 3JCUO 5B5EO 5E79O 5GTHO 3WU2O 4UB6O 5G38A 4UB8O 4PJ0O
chains in the Genus database with same CATH homology


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

 
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