4NWJ | Genus

Total Genus 189

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	189
Knots found	KnotProt 2.0: S +3₁
sequence length	504
structure length	504
Chain Sequence	AKKPTALIILDGFANRESEHGNAVKLANKPNFDRYYNKYPTTQIEASGLDVGLPEGQMGNSEVGHMNIGAGRIVYQSLTRINKSIEDGDFFENDVLNNAIAHVNSHDSALHIFGLLSDGGVHSHYKHLFALLELAKKQGVEKVYVHAFLDGRDVDQKSALKYIEETEAKFNELGIGQFASVSGRYYAMDRDKRWEREEKAYNAIRNFDAPTYATAKEGVEASYNEGLTDEFVVPFIVENQNDGVNDGDAVIFYNFRPDRAAQLSEIFANRAFEGFKVEQVKDLFYATFTKYNDNIDAAIVFEKVDLNNTIGEIAQNNNLTQLRIAETEKYPHVTYFMSGGRNEEFKGERRRLIDSPKVATYDLKPEMSAYEVKDALLEELNKGDLDLIILNFANPDMVGHSGMLEPTIKAIEAVDECLGEVVDKILDMDGYAIITADHGNSDQVLTDDDQPMTTHTTNPVPVIVTKEGVTLRETGRLGDLAPTLLDLLNVEQPEDMTGESLIKH

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/5d00887d6775487c7fa26182/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d00887d6775487c7fa26182/pdb.gz): 1183 ms

reading 504 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

504 atoms created

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

Time for creating model: 54 ms

Adding embedded #jmolscript: select ({0:503});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	189
structure length	504
sequence length	504
other databases	KnotProt 2.0: S +3₁
ec nomenclature	ec 5.4.2.12: Phosphoglycerate mutase (2,3-diphosphoglycerate-independent).
pdb deposition date	2013-12-06

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	4nwjA01
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	4nwjA02

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

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

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)

4NWJA

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations