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


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

 
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