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


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

 
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