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


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