1K35 | Genus

Total Genus 151

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	151
sequence length	455
structure length	454
Chain Sequence	LPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGHNPPDYNGFKIVVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF

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

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The Resolver thinks Pdb

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Time for openFile(/file/5cfb6dca8bdc61a0b01ff2de/pdb.gz): 1577 ms

reading 454 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

454 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 29 ms

Adding embedded #jmolscript: select ({0:453});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Isomerase
source organism	Pseudomonas aeruginosa
publication title	Crystal structure of PMM/PGM: an enzyme in the biosynthetic pathway of P. aeruginosa virulence factors. pubmed doi rcsb
molecule keywords	Phosphomannomutase
total genus	151
structure length	454
sequence length	455
ec nomenclature	ec 5.4.2.2: Phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent).
pdb deposition date	2001-10-01

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00408	PGM_PMM_IV	Phosphoglucomutase/phosphomannomutase, C-terminal domain
A	PF02878	PGM_PMM_I	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
A	PF02879	PGM_PMM_II	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
A	PF02880	PGM_PMM_III	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.30.310.50	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	Alpha-D-phosphohexomutase, C-terminal domain	1k35A04
3.40.120.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3	Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3	1k35A03
3.40.120.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3	Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3	1k35A01
3.40.120.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3	Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3	1k35A02

4MRQA 2FUVA 5JN5A 5BMNA 5KL0A 1P5GX 1K35A 1P5DX 4WX8A 5BMPA 2JPIA 3NA5A 3UW2A 2EIUA 2FKMX 4QG5A 4IL8A 1PCJX 1C4GA 3PDKA 2DKAA 2DKCA 4WXAA 2H5AX 1TUOA 3ENOC 3OLPA 1LXTA 2Z0FA 5JMVD 1KFQA 5F9CA 5HSHA 1JDYA 3C04A 1KFIA 2DKDA 1WJWA 3PMGA 3RSMA 4BJUA 3I3WA 1PCMX 3BKQX 1K2YX 1VKLA 5EPCA 3ENCA 1WQAA 2FKFA 2EHPA 2H4LX 4HJHA 1C47A 2F7LA
chains in the Genus database with same CATH superfamily

1YTFA 5JN5A 3EIKA 5BMNA 3OH6A 5KL0A 1LWVA 1UT4A 1TGHA 1QTSA 3N89A 1C9BB 2NOBA 4ROCB 1P5DX 1QN6A 3OCIA 3NA5A 3H1ZA 5IYBP 1QNBA 2HL9A 2D0AA 2I5WA 4EJYA 2NOLA 1E42A 1M5Q1 2VJ0A 4QG5A 2EIUA 3PDKA 2R5XA 3IH7A 5IYDP 1MPGA 3ENOC 1V5SA 1AISA 1QN8A 1KFQA 1T6AA 4B0AA 4EAKA 1M3QA 3EAYA 3OC3C 2ZFDB 1J3MA 2O3OA 3PMGA 3RSMA 4BJUA 1N3CA 2Y8QA 3DPUA 1QN9A 2IV8A 1YTBA 2OOYA 3I3WA 2NLVA 3CW7A 1M3HA 1W80A 2YH5A 1QN4A 4C7PA 3ENCA 1HU0A 2FGTA 1QN5A 3OSMA 4HJHA 4D7QA 3I0WA 1PZDA 1VTOA 2FUVA 2MZ8A 3VN5A 4TPSA 2NOHA 1P5GX 1FN7A 1QN7A 4WX8A 2NOFA 2HL8A 4CFFA 3CWTA 2XHIA 1CDWA 4DULA 3CVSA 1JFIC 4ROEB 3CWAA 3CWSA 1YQLA 2DKCA 2JHNA 1LWYA 2H5AX 1TUOA 3OLPA 1EBMA 1UT7A 5F9CA 3HS9A 3OH9A 3OSTA 2V92A 1KYUA 3C04A 1KO9A 2Y8LA 3ASMA 4PY5A 2V8QA 1KY6A 1QN3A 3RPJA 1TBPA 3BKQX 4Q11A 1R4XA 2JHJA 3F10A 3OGDA 2OOXA 5EPCA 2NOZA 1QTPA 1MP9A 3TDHA 1N3AA 1DIZA 2NOEA 1NGMA 4EAJA 2QRDA 1YQMA 2G30A 1LWWA 2NWVA 5AN4A 3CVTA 1K35A 1RM1A 2JPIA 1PCZA 1KY7A 3UW2A 2FKMX 1KYFA 4IL8A 1XSZA 4D7RA 4EAGA 4EALA 1EUVA 1VOLB 1B9KA 4EAIA 2NOIA 1JDYA 1UL7A 1KFIA 1WJWA 2Z8UA 2NVMA 3OSEA 3T4NA 1PCMX 2D0CA 1VKLA 2YA3A 2HKPA 4RODB 1NH2A 2PWWA 2EHPA 1QNEA 2F7LA 3TE5A 4MRQA 3SNSA 3D4VA 4I8OA 2EHBD 2HZMA 2JOIA 3CWUA 2LAEA 1QNCA 1YQRA 5BMPA 2D0BA 2QREA 3KTUA 1NVPA 3KRMA 1PCJX 1C4GA 2QR1A 3ULXA 1PVSA 1TBAB 3D7QA 2DKAA 2QLVA 3DPTA 4WXAA 5IYCP 1D3UA 1KYDA 1N39A 1LXTA 2HZSA 2Z0FA 5JMVD 1YQKA 5HSHA 1Q9UA 3I0XA 2DKDA 4EJZA 2MJ7A 3HS8A 1QNAA 1K2YX 2V9JA 2IV9A 1VOKA 1WQAA 2FKFA 4WZSD 2H4LX 3F0ZA 2QRCA 1VTLE 1C47A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4MRQ A;  2FUV A;  5JN5 A;  5BMN A;  5KL0 A;  1P5G X;  1K35 A;  1P5D X;  4WX8 A;  5BMP A;  2JPI A;  3NA5 A;  3UW2 A;  2EIU A;  2FKM X;  4QG5 A;  4IL8 A;  1PCJ X;  1C4G A;  3PDK A;  2DKA A;  2DKC A;  4WXA A;  2H5A X;  1TUO A;  3ENO C;  3OLP A;  1LXT A;  2Z0F A;  5JMV D;  1KFQ A;  5F9C A;  5HSH A;  1JDY A;  3C04 A;  1KFI A;  2DKD A;  1WJW A;  3PMG A;  3RSM A;  4BJU A;  3I3W A;  1PCM X;  3BKQ X;  1K2Y X;  1VKL A;  5EPC A;  3ENC A;  1WQA A;  2FKF A;  2EHP A;  2H4L X;  4HJH A;  1C47 A;  2F7L A; 
#chains in the Genus database with same CATH topology
 1YTF A;  5JN5 A;  3EIK A;  5BMN A;  3OH6 A;  5KL0 A;  1LWV A;  1UT4 A;  1TGH A;  1QTS A;  3N89 A;  1C9B B;  2NOB A;  4ROC B;  1P5D X;  1QN6 A;  3OCI A;  3NA5 A;  3H1Z A;  5IYB P;  1QNB A;  2HL9 A;  2D0A A;  2I5W A;  4EJY A;  2NOL A;  1E42 A;  1M5Q 1;  2VJ0 A;  4QG5 A;  2EIU A;  3PDK A;  2R5X A;  3IH7 A;  5IYD P;  1MPG A;  3ENO C;  1V5S A;  1AIS A;  1QN8 A;  1KFQ A;  1T6A A;  4B0A A;  4EAK A;  1M3Q A;  3EAY A;  3OC3 C;  2ZFD B;  1J3M A;  2O3O A;  3PMG A;  3RSM A;  4BJU A;  1N3C A;  2Y8Q A;  3DPU A;  1QN9 A;  2IV8 A;  1YTB A;  2OOY A;  3I3W A;  2NLV A;  3CW7 A;  1M3H A;  1W80 A;  2YH5 A;  1QN4 A;  4C7P A;  3ENC A;  1HU0 A;  2FGT A;  1QN5 A;  3OSM A;  4HJH A;  4D7Q A;  3I0W A;  1PZD A;  1VTO A;  2FUV A;  2MZ8 A;  3VN5 A;  4TPS A;  2NOH A;  1P5G X;  1FN7 A;  1QN7 A;  4WX8 A;  2NOF A;  2HL8 A;  4CFF A;  3CWT A;  2XHI A;  1CDW A;  4DUL A;  3CVS A;  1JFI C;  4ROE B;  3CWA A;  3CWS A;  1YQL A;  2DKC A;  2JHN A;  1LWY A;  2H5A X;  1TUO A;  3OLP A;  1EBM A;  1UT7 A;  5F9C A;  3HS9 A;  3OH9 A;  3OST A;  2V92 A;  1KYU A;  3C04 A;  1KO9 A;  2Y8L A;  3ASM A;  4PY5 A;  2V8Q A;  1KY6 A;  1QN3 A;  3RPJ A;  1TBP A;  3BKQ X;  4Q11 A;  1R4X A;  2JHJ A;  3F10 A;  3OGD A;  2OOX A;  5EPC A;  2NOZ A;  1QTP A;  1MP9 A;  3TDH A;  1N3A A;  1DIZ A;  2NOE A;  1NGM A;  4EAJ A;  2QRD A;  1YQM A;  2G30 A;  1LWW A;  2NWV A;  5AN4 A;  3CVT A;  1K35 A;  1RM1 A;  2JPI A;  1PCZ A;  1KY7 A;  3UW2 A;  2FKM X;  1KYF A;  4IL8 A;  1XSZ A;  4D7R A;  4EAG A;  4EAL A;  1EUV A;  1VOL B;  1B9K A;  4EAI A;  2NOI A;  1JDY A;  1UL7 A;  1KFI A;  1WJW A;  2Z8U A;  2NVM A;  3OSE A;  3T4N A;  1PCM X;  2D0C A;  1VKL A;  2YA3 A;  2HKP A;  4ROD B;  1NH2 A;  2PWW A;  2EHP A;  1QNE A;  2F7L A;  3TE5 A;  4MRQ A;  3SNS A;  3D4V A;  4I8O A;  2EHB D;  2HZM A;  2JOI A;  3CWU A;  2LAE A;  1QNC A;  1YQR A;  5BMP A;  2D0B A;  2QRE A;  3KTU A;  1NVP A;  3KRM A;  1PCJ X;  1C4G A;  2QR1 A;  3ULX A;  1PVS A;  1TBA B;  3D7Q A;  2DKA A;  2QLV A;  3DPT A;  4WXA A;  5IYC P;  1D3U A;  1KYD A;  1N39 A;  1LXT A;  2HZS A;  2Z0F A;  5JMV D;  1YQK A;  5HSH A;  1Q9U A;  3I0X A;  2DKD A;  4EJZ A;  2MJ7 A;  3HS8 A;  1QNA A;  1K2Y X;  2V9J A;  2IV9 A;  1VOK A;  1WQA A;  2FKF A;  4WZS D;  2H4L X;  3F0Z A;  2QRC A;  1VTL E;  1C47 A; 
#chains in the Genus database with same CATH homology
 4MRQ A;  2FUV A;  5JN5 A;  5BMN A;  5KL0 A;  1P5G X;  1K35 A;  1P5D X;  4WX8 A;  5BMP A;  2JPI A;  3NA5 A;  3UW2 A;  2EIU A;  2FKM X;  4QG5 A;  4IL8 A;  1PCJ X;  1C4G A;  3PDK A;  2DKA A;  2DKC A;  4WXA A;  2H5A X;  1TUO A;  3ENO C;  3OLP A;  1LXT A;  2Z0F A;  5JMV D;  1KFQ A;  5F9C A;  5HSH A;  1JDY A;  3C04 A;  1KFI A;  2DKD A;  1WJW A;  3PMG A;  3RSM A;  4BJU A;  3I3W A;  1PCM X;  3BKQ X;  1K2Y X;  1VKL A;  5EPC A;  3ENC A;  1WQA A;  2FKF A;  2EHP A;  2H4L X;  4HJH A;  1C47 A;  2F7L A;

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similar chains in the Genus database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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1K35A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations