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


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

 
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