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


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