1O99 | Genus

Total Genus 195

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	195
Knots found	KnotProt 2.0: S +3₁
sequence length	509
structure length	509
Chain Sequence	SKKPVALIILDGFALRDETYGNAVAQANKPNFDRYWNEYPHTTLKACGEAVGLPEGQMGNAEVGHLNIGAGRIVYQSLTRINIAIREGEFDRNETFLAAMNHVKQHGTSLHLFGLLSDGGVHSHIHHLYALLRLAAKEGVKRVYIHGFLDGRDVGPQTAPQYIKELQEKIKEYGVGEIATLSGRYYSMDRDKRWDRVEKAYRAMVYGEGPTYRDPLECIEDSYKHGIYDEFVLPSVIVREDGRPVATIQDNDAIIFYNFRPDRAIQISNTFTNEDFREFDRGPKHPKHLFFVCLTHFSETVAGYVAFKPTNLDNTIGEVLSQHGLRQLRIAETEKYPHVTFFMSGGREEEFPGEDRILINSPKVPTYDLKPEMSAYEVTDALLKEIEADKYDAIILNYANPDMVGHSGKLEPTIKAVEAVDECLGKVVDAILAKGGIAIITADHGNADEVLTPDGKPQTAHTTNPVPVIVTKKGIKLRDGGILGDLAPTMLDLLGLPQPKEMTGKSLIV

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

loadScript /static/js/j2s/core/package.js

loadScript /static/js/j2s/core/corejmol.z.js

loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__126647150693405__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__126647150693405__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1o99/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__126647150693405__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"126647150693405","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1o99/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__126647150693405__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfbb88f54417e14febbc1e4/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfbb88f54417e14febbc1e4/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfbb88f54417e14febbc1e4/pdb.gz)

loadScript /static/js/j2s/core/corezip.z.js

The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5cfbb88f54417e14febbc1e4/pdb.gz): 1979 ms

reading 509 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

509 atoms created

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

Time for creating model: 33 ms

Adding embedded #jmolscript: select ({0:508});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

publication title	Insights Into the Catalytic Mechanism of Cofactor-Independent Phosphoglycerate Mutase from X-Ray Crystallography, Simulated Dynamics and Molecular Modeling pubmed doi rcsb
molecule keywords	2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE
molecule tags	Isomerase
source organism	Bacillus stearothermophilus
total genus	195
structure length	509
sequence length	509
other databases	KnotProt 2.0: S +3₁
ec nomenclature	ec 5.4.2.12: Phosphoglycerate mutase (2,3-diphosphoglycerate-independent).
pdb deposition date	2002-12-11

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	1o99A02
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	1o99A01

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

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

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

1O99A

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations