4MY4 | Genus

Total Genus 192

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	192
Knots found	KnotProt 2.0: S +3₁
sequence length	503
structure length	503
Chain Sequence	KKPTALIILDGFANRESEHGNAVKLANKPNFDRYYNKYPTTQIEASGLDVGLPEGQMGNSEVGHMNIGAGRIVYQSLTRINKSIEDGDFFENDVLNNAIAHVNSHDSALHIFGLLSDGGVHSHYKHLFALLELAKKQGVEKVYVHAFLDGRDVDQKSALKYIEETEAKFNELGIGQFASVSGRYYAMDRDKRWEREEKAYNAIRNFDAPTYATAKEGVEASYNEGLTDEFVVPFIVENQNDGVNDGDAVIFYNFRPDRAAQLSEIFANRAFEGFKVEQVKDLFYATFTKYNDNIDAAIVFEKVDLNNTIGEIAQNNNLTQLRIAETEKYPHVTYFMSGGRNEEFKGERRRLIDSPKVATYDLKPEMSAYEVKDALLEELNKGDLDLIILNFANPDMVGHSGMLEPTIKAIEAVDECLGEVVDKILDMDGYAIITADHGNSDQVLTDDDQPMTTHTTNPVPVIVTKEGVTLRETGRLGDLAPTLLDLLNVEQPEDMTGESLIKH

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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Viewer cachePut cache://localLOAD_/file/5d007ff63665ad2917effdae/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d007ff63665ad2917effdae/pdb.gz): 1225 ms

reading 503 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

503 atoms created

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

Time for creating model: 42 ms

Adding embedded #jmolscript: select ({0:502});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

publication title	Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism pubmed doi rcsb
molecule keywords	2,3-bisphosphoglycerate-independent phosphoglycerate mutase
molecule tags	Isomerase
source organism	Staphylococcus aureus subsp. aureus
total genus	192
structure length	503
sequence length	503
other databases	KnotProt 2.0: S +3₁
ec nomenclature	ec 5.4.2.1: Transferred entry: 5.4.2.11 and 5.4.2.12.
pdb deposition date	2013-09-27

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01676	Metalloenzyme	Metalloenzyme superfamily
A	PF06415	iPGM_N	BPG-independent PGAM N-terminus (iPGM_N)

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.720.10	Alpha Beta	3-Layer(aba) Sandwich	Alkaline Phosphatase, subunit A	Alkaline Phosphatase, subunit A	4my4A01
3.40.1450.10	Alpha Beta	3-Layer(aba) Sandwich	2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain	BPG-independent phosphoglycerate mutase, domain B	4my4A02

1AUKA 3MK0A 3MK2A 2W5QA 5INHA 4UPIA 1ELZA 4GTXA 4LRAA 1KHNA 3NKNA 2D1GA 3WAYA 4N7TA 2ZKTA 4LRBA 4LRDA 1E2SP 1P49A 4KJGA 5IJQA 5LIAA 4UPLA 1AJBA 4TN0A 4GTYA 4LR8A 3NKMA 4GTZA 3TG0A 3Q3QA 5EGEA 3DYCA 3UNYA 5L0BA 1HJKA 3NVLA 2W8SA 4ZG6A 3M7VA 2W5RA 3E2DA 3M8WA 1ALJA 3BDHA 1O98A 3T00A 2W8DA 2XRGA 5EGHA 1ANIA 3A52A 4ZG9A 5KXAA 3MK1A 5AJ9A 5GOVA 1Y6VA 3WAVA 4B56A 3M8ZA 4UOPA 1URAA 1EW8A 1E33P 4MHXA 3BDFA 1ZEDA 1B8JA 4GTWA 4MIVA 5TJ3A 4LREA 3SZZA 1ED8A 1ZEFA 2IUCA 1E1ZP 2W5WA 1ELYA 1O99A 5K4PA 1ALHA 5LRNA 3DPCA 1AJCA 4UOOA 3UN2A 1KH4A 3TWZA 3OT9A 4LQYA 1ALKA 3LXQA 4CXSA 1EJJA 4ZG7A 2W5VA 5DLTA 4LRCA 1URBA 5GRRA 5IJSA 5DLVA 4KAVA 1ANJA 1KHJA 2GSOA 2ANHA 1KHKA 3WAXA 4ZGAA 4NWJA 3NKOA 2G9YA 3T02A 2W5SA 2XR9A 2GA3A 3BDGB 1KH7A 2IFYA 1N2LA 4UORA 3WBHA 5C66A 2QZUA 3TX0A 3CMRA 1ED9A 1EW2A 4FDJA 2W5XA 2W5TA 4KJDA 4KM4A 2GLQA 3B5QA 4UPHA 1AJDA 5DLWA 1AJAA 3NKPA 1KH5A 3ED4A 1ELXA 3T01A 5L0KA 4CXKA 4LR7A 1KH9A 4LR2A 2VQRA 1K7HA 1KHLA 4MY4A 4UPKA 4LR9A 5HRTA 3IGZB 1EW9A 1SHQA 3BDGA 4CYSA 3KD8A 4NWXA 1EQJA 3NKRA 5LRMA 4FDIA 4QAXA 4LRFA 2GSNA 3M8YA 4YR1A 3UO0A 2IUCB 5LQQA 2X98A 1HDHA 3WAWA 1ALIA 1HQAA 1E3CP 4KAYA 3NKQA 1Y7AA 1FSUA 4CYRA 3SZYA 1ZEBA 1EI6A 3IDDA 4CXUA 2RH6A 1SHNA 1N2KA 2GSUA 3UN3A 3UN5A 5L0EA 3IGYB
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1AUK A;  3MK0 A;  3MK2 A;  2W5Q A;  5INH A;  4UPI A;  1ELZ A;  4GTX A;  4LRA A;  1KHN A;  3NKN A;  2D1G A;  3WAY A;  4N7T A;  2ZKT A;  4LRB A;  4LRD A;  1E2S P;  1P49 A;  4KJG A;  5IJQ A;  5LIA A;  4UPL A;  1AJB A;  4TN0 A;  4GTY A;  4LR8 A;  3NKM A;  4GTZ A;  3TG0 A;  3Q3Q A;  5EGE A;  3DYC A;  3UNY A;  5L0B A;  1HJK A;  3NVL A;  2W8S A;  4ZG6 A;  3M7V A;  2W5R A;  3E2D A;  3M8W A;  1ALJ A;  3BDH A;  1O98 A;  3T00 A;  2W8D A;  2XRG A;  5EGH A;  1ANI A;  3A52 A;  4ZG9 A;  5KXA A;  3MK1 A;  5AJ9 A;  5GOV A;  1Y6V A;  3WAV A;  4B56 A;  3M8Z A;  4UOP A;  1URA A;  1EW8 A;  1E33 P;  4MHX A;  3BDF A;  1ZED A;  1B8J A;  4GTW A;  4MIV A;  5TJ3 A;  4LRE A;  3SZZ A;  1ED8 A;  1ZEF A;  2IUC A;  1E1Z P;  2W5W A;  1ELY A;  1O99 A;  5K4P A;  1ALH A;  5LRN A;  3DPC A;  1AJC A;  4UOO A;  3UN2 A;  1KH4 A;  3TWZ A;  3OT9 A;  4LQY A;  1ALK A;  3LXQ A;  4CXS A;  1EJJ A;  4ZG7 A;  2W5V A;  5DLT A;  4LRC A;  1URB A;  5GRR A;  5IJS A;  5DLV A;  4KAV A;  1ANJ A;  1KHJ A;  2GSO A;  2ANH A;  1KHK A;  3WAX A;  4ZGA A;  4NWJ A;  3NKO A;  2G9Y A;  3T02 A;  2W5S A;  2XR9 A;  2GA3 A;  3BDG B;  1KH7 A;  2IFY A;  1N2L A;  4UOR A;  3WBH A;  5C66 A;  2QZU A;  3TX0 A;  3CMR A;  1ED9 A;  1EW2 A;  4FDJ A;  2W5X A;  2W5T A;  4KJD A;  4KM4 A;  2GLQ A;  3B5Q A;  4UPH A;  1AJD A;  5DLW A;  1AJA A;  3NKP A;  1KH5 A;  3ED4 A;  1ELX A;  3T01 A;  5L0K A;  4CXK A;  4LR7 A;  1KH9 A;  4LR2 A;  2VQR A;  1K7H A;  1KHL A;  4MY4 A;  4UPK A;  4LR9 A;  5HRT A;  3IGZ B;  1EW9 A;  1SHQ A;  3BDG A;  4CYS A;  3KD8 A;  4NWX A;  1EQJ A;  3NKR A;  5LRM A;  4FDI A;  4QAX A;  4LRF A;  2GSN A;  3M8Y A;  4YR1 A;  3UO0 A;  2IUC B;  5LQQ A;  2X98 A;  1HDH A;  3WAW A;  1ALI A;  1HQA A;  1E3C P;  4KAY A;  3NKQ A;  1Y7A A;  1FSU A;  4CYR A;  3SZY A;  1ZEB A;  1EI6 A;  3IDD A;  4CXU A;  2RH6 A;  1SHN A;  1N2K A;  2GSU A;  3UN3 A;  3UN5 A;  5L0E A;  3IGY B; 
#chains in the Genus database with same CATH topology
 1AUK A;  3MK0 A;  3MK2 A;  2W5Q A;  5INH A;  4UPI A;  1ELZ A;  4GTX A;  4LRA A;  1KHN A;  3NKN A;  2D1G A;  3WAY A;  4N7T A;  2ZKT A;  4LRB A;  4LRD A;  1E2S P;  1P49 A;  4KJG A;  5IJQ A;  5LIA A;  4UPL A;  1AJB A;  4TN0 A;  4GTY A;  4LR8 A;  3NKM A;  4GTZ A;  3TG0 A;  3Q3Q A;  5EGE A;  3DYC A;  3UNY A;  5L0B A;  1HJK A;  3NVL A;  2W8S A;  4ZG6 A;  3M7V A;  2W5R A;  3E2D A;  3M8W A;  1ALJ A;  3BDH A;  1O98 A;  3T00 A;  2W8D A;  2XRG A;  5EGH A;  1ANI A;  3A52 A;  4ZG9 A;  5KXA A;  3MK1 A;  5AJ9 A;  5GOV A;  1Y6V A;  3WAV A;  4B56 A;  3M8Z A;  4UOP A;  1URA A;  1EW8 A;  1E33 P;  4MHX A;  3BDF A;  1ZED A;  1B8J A;  4GTW A;  4MIV A;  5TJ3 A;  4LRE A;  3SZZ A;  1ED8 A;  1ZEF A;  2IUC A;  1E1Z P;  2W5W A;  1ELY A;  1O99 A;  5K4P A;  1ALH A;  5LRN A;  3DPC A;  1AJC A;  4UOO A;  3UN2 A;  1KH4 A;  3TWZ A;  3OT9 A;  4LQY A;  1ALK A;  3LXQ A;  4CXS A;  1EJJ A;  4ZG7 A;  2W5V A;  5DLT A;  4LRC A;  1URB A;  5GRR A;  5IJS A;  5DLV A;  4KAV A;  1ANJ A;  1KHJ A;  2GSO A;  2ANH A;  1KHK A;  3WAX A;  4ZGA A;  4NWJ A;  3NKO A;  2G9Y A;  3T02 A;  2W5S A;  2XR9 A;  2GA3 A;  3BDG B;  1KH7 A;  2IFY A;  1N2L A;  4UOR A;  3WBH A;  5C66 A;  2QZU A;  3TX0 A;  3CMR A;  1ED9 A;  1EW2 A;  4FDJ A;  2W5X A;  2W5T A;  4KJD A;  4KM4 A;  2GLQ A;  3B5Q A;  4UPH A;  1AJD A;  5DLW A;  1AJA A;  3NKP A;  1KH5 A;  3ED4 A;  1ELX A;  3T01 A;  5L0K A;  4CXK A;  4LR7 A;  1KH9 A;  4LR2 A;  2VQR A;  1K7H A;  1KHL A;  4MY4 A;  4UPK A;  4LR9 A;  5HRT A;  3IGZ B;  1EW9 A;  1SHQ A;  3BDG A;  4CYS A;  3KD8 A;  4NWX A;  1EQJ A;  3NKR A;  5LRM A;  4FDI A;  4QAX A;  4LRF A;  2GSN A;  3M8Y A;  4YR1 A;  3UO0 A;  2IUC B;  5LQQ A;  2X98 A;  1HDH A;  3WAW A;  1ALI A;  1HQA A;  1E3C P;  4KAY A;  3NKQ A;  1Y7A A;  1FSU A;  4CYR A;  3SZY A;  1ZEB A;  1EI6 A;  3IDD A;  4CXU A;  2RH6 A;  1SHN A;  1N2K A;  2GSU A;  3UN3 A;  3UN5 A;  5L0E A;  3IGY B; 
#chains in the Genus database with same CATH homology
 1AUK A;  3MK0 A;  3MK2 A;  2W5Q A;  5INH A;  4UPI A;  1ELZ A;  4GTX A;  4LRA A;  1KHN A;  3NKN A;  2D1G A;  3WAY A;  4N7T A;  2ZKT A;  4LRB A;  4LRD A;  1E2S P;  1P49 A;  4KJG A;  5IJQ A;  5LIA A;  4UPL A;  1AJB A;  4TN0 A;  4GTY A;  4LR8 A;  3NKM A;  4GTZ A;  3TG0 A;  3Q3Q A;  5EGE A;  3DYC A;  3UNY A;  5L0B A;  1HJK A;  3NVL A;  2W8S A;  4ZG6 A;  3M7V A;  2W5R A;  3E2D A;  3M8W A;  1ALJ A;  3BDH A;  1O98 A;  3T00 A;  2W8D A;  2XRG A;  5EGH A;  1ANI A;  3A52 A;  4ZG9 A;  5KXA A;  3MK1 A;  5AJ9 A;  5GOV A;  1Y6V A;  3WAV A;  4B56 A;  3M8Z A;  4UOP A;  1URA A;  1EW8 A;  1E33 P;  4MHX A;  3BDF A;  1ZED A;  1B8J A;  4GTW A;  4MIV A;  5TJ3 A;  4LRE A;  3SZZ A;  1ED8 A;  1ZEF A;  2IUC A;  1E1Z P;  2W5W A;  1ELY A;  1O99 A;  5K4P A;  1ALH A;  5LRN A;  3DPC A;  1AJC A;  4UOO A;  3UN2 A;  1KH4 A;  3TWZ A;  3OT9 A;  4LQY A;  1ALK A;  3LXQ A;  4CXS A;  1EJJ A;  4ZG7 A;  2W5V A;  5DLT A;  4LRC A;  1URB A;  5GRR A;  5IJS A;  5DLV A;  4KAV A;  1ANJ A;  1KHJ A;  2GSO A;  2ANH A;  1KHK A;  3WAX A;  4ZGA A;  4NWJ A;  3NKO A;  2G9Y A;  3T02 A;  2W5S A;  2XR9 A;  2GA3 A;  3BDG B;  1KH7 A;  2IFY A;  1N2L A;  4UOR A;  3WBH A;  5C66 A;  2QZU A;  3TX0 A;  3CMR A;  1ED9 A;  1EW2 A;  4FDJ A;  2W5X A;  2W5T A;  4KJD A;  4KM4 A;  2GLQ A;  3B5Q A;  4UPH A;  1AJD A;  5DLW A;  1AJA A;  3NKP A;  1KH5 A;  3ED4 A;  1ELX A;  3T01 A;  5L0K A;  4CXK A;  4LR7 A;  1KH9 A;  4LR2 A;  2VQR A;  1K7H A;  1KHL A;  4MY4 A;  4UPK A;  4LR9 A;  5HRT A;  3IGZ B;  1EW9 A;  1SHQ A;  3BDG A;  4CYS A;  3KD8 A;  4NWX A;  1EQJ A;  3NKR A;  5LRM A;  4FDI A;  4QAX A;  4LRF A;  2GSN A;  3M8Y A;  4YR1 A;  3UO0 A;  2IUC B;  5LQQ A;  2X98 A;  1HDH A;  3WAW A;  1ALI A;  1HQA A;  1E3C P;  4KAY A;  3NKQ A;  1Y7A A;  1FSU A;  4CYR A;  3SZY A;  1ZEB A;  1EI6 A;  3IDD A;  4CXU A;  2RH6 A;  1SHN A;  1N2K A;  2GSU A;  3UN3 A;  3UN5 A;  5L0E A;  3IGY B;

1EJJA 1EQJA 1O98A 1O99A 2IFYA 4NWJA 4NWXA 4QAXA 7TL8A
similar chains in the Genus database (40% sequence similarity)

None
similar chains in the pdb database (40% sequence similarity)

#similar chains in the Genus database (40% sequence similarity)
1EJJ A; 1EQJ A; 1O98 A; 1O99 A; 2IFY A; 4NWJ A; 4NWX A; 4QAX A; 7TL8 A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)

4MY4A

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations