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


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

 
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