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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   ASYMMETRIC COMPLEX OF HUMAN NEURON SPECIFIC ENOLASE-5-PGA/PEP

Authors :   J. Qin, G. Chai, J. Brewer, L. Lovelace, L. Lebioda

Date :   08 Nov 11 (Deposition) - 22 Aug 12 (Release) - 22 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Qin, G. Chai, J. M. Brewer, L. L. Lovelace, L. Lebioda
Structures Of Asymmetric Complexes Of Human Neuron Specific Enolase With Resolved Substrate And Product And An Analogou Complex With Two Inhibitors Indicate Subunit Interaction An Inhibitor Cooperativity.
J. Inorg. Biochem. V. 111 187 2012
PubMed-ID: 22437160 | Reference-DOI: 10.1016/J.JINORGBIO.2012.02.011

Molecule 1 - GAMMA-ENOLASE
	Chains	:	A, B
	EC Number	:	4.2.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ENO2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	2-PHOSPHO-D-GLYCERATE HYDRO-LYASE, ENOLASE 2, NEURAL ENOLASE, NEURON-SPECIFIC ENOLASE, NSE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	2PG	1	Ligand/Ion	2-PHOSPHOGLYCERIC ACID
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	PEP	1	Ligand/Ion	PHOSPHOENOLPYRUVATE
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:244 , GLU A:292 , ASP A:317 , 2PG A:503 , HOH A:601	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	SER A:39 , 2PG A:503 , HOH A:602 , HOH A:603	BINDING SITE FOR RESIDUE MG A 502
3	AC3	SOFTWARE	GLY A:37 , ALA A:38 , SER A:39 , HIS A:157 , GLN A:165 , GLU A:166 , GLU A:209 , ASP A:244 , GLU A:292 , ASP A:317 , LEU A:340 , LYS A:342 , HIS A:370 , ARG A:371 , SER A:372 , LYS A:393 , MG A:501 , MG A:502 , HOH A:602 , HOH A:603	BINDING SITE FOR RESIDUE 2PG A 503
4	AC4	SOFTWARE	THR A:40 , ILE A:42 , SER A:248 , GLU A:249 , GLN A:297 , HOH A:677 , HOH A:721 , HOH A:728 , HOH A:875	BINDING SITE FOR RESIDUE TRS A 504
5	AC5	SOFTWARE	ASP B:244 , GLU B:292 , ASP B:317 , LYS B:393 , PEP B:503 , HOH B:601	BINDING SITE FOR RESIDUE MG B 501
6	AC6	SOFTWARE	SER B:39 , PEP B:503 , HOH B:602 , HOH B:603	BINDING SITE FOR RESIDUE MG B 502
7	AC7	SOFTWARE	GLY B:37 , ALA B:38 , SER B:39 , GLN B:165 , GLU B:166 , GLU B:209 , ASP B:244 , GLU B:292 , ASP B:317 , LEU B:340 , LYS B:342 , ARG B:371 , SER B:372 , LYS B:393 , MG B:501 , MG B:502 , HOH B:602 , HOH B:603	BINDING SITE FOR RESIDUE PEP B 503

(no "SS Bond" information available for 3UJR)

(no "Cis Peptide Bond" information available for 3UJR)

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_002354	P	264	A	ENOG_HUMAN	Polymorphism	---	A/B	P	263	A
2	UniProt	VAR_002355	T	395	A	ENOG_HUMAN	Polymorphism	---	A/B	T	394	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOLASE	PS00164	Enolase signature.	ENOG_HUMAN	340-353	2	A:339-352 B:339-352

Asymmetric/Biological Unit (11, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000229277	1	ENSE00001102855	chr12:7023614-7023823	210	ENOG_HUMAN	-	0	0	-	-
1.2	ENST00000229277	2	ENSE00001164484	chr12:7024985-7025081	97	ENOG_HUMAN	1-29	29	2	A:1-28 B:1-28	28 28
1.3	ENST00000229277	3	ENSE00000716175	chr12:7025581-7025676	96	ENOG_HUMAN	29-61	33	2	A:28-60 B:28-60	33 33
1.4	ENST00000229277	4	ENSE00000716176	chr12:7025835-7025893	59	ENOG_HUMAN	61-80	20	2	A:60-79 B:60-79	20 20
1.5	ENST00000229277	5	ENSE00000716177	chr12:7026202-7026271	70	ENOG_HUMAN	81-104	24	2	A:80-103 B:80-103	24 24
1.6	ENST00000229277	6	ENSE00000716178	chr12:7026745-7026878	134	ENOG_HUMAN	104-148	45	2	A:103-147 B:103-147	45 45
1.7	ENST00000229277	7	ENSE00001727933	chr12:7027104-7027326	223	ENOG_HUMAN	149-223	75	2	A:148-222 B:148-222	75 75
1.8	ENST00000229277	8	ENSE00000716183	chr12:7028730-7028927	198	ENOG_HUMAN	223-289	67	2	A:222-288 B:222-288	67 67
1.9	ENST00000229277	9	ENSE00000716184	chr12:7030744-7030945	202	ENOG_HUMAN	289-356	68	2	A:288-355 B:288-355	68 68
1.10	ENST00000229277	10	ENSE00001724735	chr12:7031219-7031327	109	ENOG_HUMAN	356-392	37	2	A:355-391 B:355-391	37 37
1.11	ENST00000229277	11	ENSE00001748845	chr12:7031507-7031565	59	ENOG_HUMAN	393-412	20	2	A:392-411 B:392-411	20 20
1.12	ENST00000229277	12	ENSE00001102828	chr12:7031894-7032859	966	ENOG_HUMAN	412-434	23	2	A:411-433 B:411-432	23 22

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:433
 aligned with ENOG_HUMAN | P09104 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:433
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431   
           ENOG_HUMAN     2 SIEKIWAREILDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDGDKQRYLGKGVLKAVDHINSTIAPALISSGLSVVEQEKLDNLMLELDGTENKSKFGANAILGVSLAVCKAGAAERELPLYRHIAQLAGNSDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGAESFRDAMRLGAEVYHTLKGVIKDKYGKDATNVGDEGGFAPNILENSEALELVKEAIDKAGYTEKIVIGMDVAASEFYRDGKYDLDFKSPTDPSRYITGDQLGALYQDFVRDYPVVSIEDPFDQDDWAAWSKFTANVGIQIVGDDLTVTNPKRIERAVEEKACNCLLLKVNQIGSVTEAIQACKLAQENGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEELGDEARFAGHNFRNPSVL 434
               SCOP domains d3ujra1 A:1-139 Enolase                                                                                                                    d3ujra2 A:140-433 Enolase                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeeee..eeeeee.....................hhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......ee.eeeee.hhhh.......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh......eeeee.hhhh.ee..ee........hhhhh.hhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhh....eeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------A--------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ENOLASE       --------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-28       -------------------------------Exon 1.4            Exon 1.5  PDB: A:80-103 --------------------------------------------Exon 1.7  PDB: A:148-222 UniProt: 149-223                                  ------------------------------------------------------------------------------------------------------------------------------------Exon 1.10  PDB: A:355-391            Exon 1.11           ---------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.3  PDB: A:28-60           ------------------------------------------Exon 1.6  PDB: A:103-147 UniProt: 104-148    --------------------------------------------------------------------------Exon 1.8  PDB: A:222-288 UniProt: 223-289                          --------------------------------------------------------------------------------------------------------------------------Exon 1.12               Transcript 1 (2)
           Transcript 1 (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:288-355 UniProt: 289-356                           ------------------------------------------------------------------------------ Transcript 1 (3)
                 3ujr A   1 SIEKIWAREILDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDGDKQRYLGKGVLKAVDHINSTIAPALISSGLSVVEQEKLDNLMLELDGTENKSKFGANAILGVSLAVCKAGAAERELPLYRHIAQLAGNSDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGAESFRDAMRLGAEVYHTLKGVIKDKYGKDATNVGDEGGFAPNILENSEALELVKEAIDKAGYTEKIVIGMDVAASEFYRDGKYDLDFKSPTDPSRYITGDQLGALYQDFVRDYPVVSIEDPFDQDDWAAWSKFTANVGIQIVGDDLTVTNPKRIERAVEEKACNCLLLKVNQIGSVTEAIQACKLAQENGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEELGDEARFAGHNFRNPSVL 433
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430

Chain B from PDB  Type:PROTEIN  Length:432
 aligned with ENOG_HUMAN | P09104 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:432
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431  
           ENOG_HUMAN     2 SIEKIWAREILDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDGDKQRYLGKGVLKAVDHINSTIAPALISSGLSVVEQEKLDNLMLELDGTENKSKFGANAILGVSLAVCKAGAAERELPLYRHIAQLAGNSDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGAESFRDAMRLGAEVYHTLKGVIKDKYGKDATNVGDEGGFAPNILENSEALELVKEAIDKAGYTEKIVIGMDVAASEFYRDGKYDLDFKSPTDPSRYITGDQLGALYQDFVRDYPVVSIEDPFDQDDWAAWSKFTANVGIQIVGDDLTVTNPKRIERAVEEKACNCLLLKVNQIGSVTEAIQACKLAQENGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEELGDEARFAGHNFRNPSV 433
               SCOP domains d3ujrb1 B:1-139 Enolase                                                                                                                    d3ujrb2 B:140-432 Enolase                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeeee..eeeeee.....................hhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.......eeeeeeee............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh......eeeee.hhhh.ee..eee.......hhh.eehhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhh...eeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------A-------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ENOLASE       -------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:1-28       -------------------------------Exon 1.4            Exon 1.5  PDB: B:80-103 --------------------------------------------Exon 1.7  PDB: B:148-222 UniProt: 149-223                                  ------------------------------------------------------------------------------------------------------------------------------------Exon 1.10  PDB: B:355-391            Exon 1.11           --------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.3  PDB: B:28-60           ------------------------------------------Exon 1.6  PDB: B:103-147 UniProt: 104-148    --------------------------------------------------------------------------Exon 1.8  PDB: B:222-288 UniProt: 223-289                          --------------------------------------------------------------------------------------------------------------------------Exon 1.12 [INCOMPLETE] Transcript 1 (2)
           Transcript 1 (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: B:288-355 UniProt: 289-356                           ----------------------------------------------------------------------------- Transcript 1 (3)
                 3ujr B   1 SIEKIWAREILDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDGDKQRYLGKGVLKAVDHINSTIAPALISSGLSVVEQEKLDNLMLELDGTENKSKFGANAILGVSLAVCKAGAAERELPLYRHIAQLAGNSDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGAESFRDAMRLGAEVYHTLKGVIKDKYGKDATNVGDEGGFAPNILENSEALELVKEAIDKAGYTEKIVIGMDVAASEFYRDGKYDLDFKSPTDPSRYITGDQLGALYQDFVRDYPVVSIEDPFDQDDWAAWSKFTANVGIQIVGDDLTVTNPKRIERAVEEKACNCLLLKVNQIGSVTEAIQACKLAQENGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEELGDEARFAGHNFRNPSV 432
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Enolase N-terminal domain-like (211)

Superfamily: Enolase N-terminal domain-like (211)

Family: Enolase N-terminal domain-like (88)

Protein domain: Enolase (39)

Human (Homo sapiens), gamma isoform [TaxId: 9606] (9)

1a	d3ujra1	A:1-139
1b	d3ujrb1	B:1-139

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Enolase C-terminal domain-like (212)

Family: Enolase (45)

Protein domain: Enolase (39)

Human (Homo sapiens), gamma isoform [TaxId: 9606] (9)

2a	d3ujra2	A:140-433
2b	d3ujrb2	B:140-432

(no "CATH Domain" information available for 3UJR)

(no "Pfam Domain" information available for 3UJR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ENOG_HUMAN | P09104)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004634	phosphopyruvate hydratase activity	Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0061621	canonical glycolysis	The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0043204	perikaryon	The portion of the cell soma (neuronal cell body) that excludes the nucleus.
	GO:0000015	phosphopyruvate hydratase complex	A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.
	GO:0001917	photoreceptor inner segment	The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	3ujr
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	4.2.1.11
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	ENOG_HUMAN \| P09104	:	1te6 2akm 2akz 3ucc 3ucd 3uje 3ujf 3ujs 4za0 4zcw 5eu9 5idz

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

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Exons (11, 22)

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