5EQD - JenaLib

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Title :   STRUCTURE OF OXIDIZED UDP-GALACTOPYRANOSE MUTASE FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH UDP IN OPENED AND CLOSED FORM

Authors :   K. Wangkanont, L. L. Kiessling, K. T. Forest

Date :   12 Nov 15 (Deposition) - 23 Nov 16 (Release) - 23 Nov 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

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

Reference :   K. Wangkanont, L. L. Kiessling, K. T. Forest
Structural Dynamics Of Udp-Galactopyranose Mutase From Mycobacterium Smegmatis
To Be Published
PubMed: search

Molecule 1 - UDP-GALACTOPYRANOSE MUTASE
	Chains	:	A, B
	EC Number	:	5.4.99.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMAL C5X
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 13-412
	Gene	:	GLF, MSMEG_6404, MSMEI_6236
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS
	Organism Taxid	:	246196
	Strain	:	ATCC 700084 / MC(2)155
	Synonym	:	UDP-GALACTOPYRANOSE MUTASE GLF

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	NO3	7	Ligand/Ion	NITRATE ION
3	SO4	6	Ligand/Ion	SULFATE ION
4	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 1 (4, 16)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	NO3	7	Ligand/Ion	NITRATE ION
3	SO4	6	Ligand/Ion	SULFATE ION
4	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	NO3	4	Ligand/Ion	NITRATE ION
3	SO4	2	Ligand/Ion	SULFATE ION
4	UDP	-1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 3 (4, 9)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	NO3	3	Ligand/Ion	NITRATE ION
3	SO4	4	Ligand/Ion	SULFATE ION
4	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:22 , GLY A:23 , GLY A:25 , PHE A:26 , PHE A:27 , ILE A:46 , GLU A:47 , ARG A:48 , ARG A:49 , GLY A:54 , ASN A:55 , TYR A:71 , ALA A:73 , HIS A:74 , LEU A:75 , THR A:232 , ASP A:233 , TRP A:234 , PHE A:235 , THR A:253 , GLY A:254 , ARG A:258 , TYR A:336 , GLY A:368 , ARG A:369 , TYR A:375 , LEU A:376 , ASP A:377 , MET A:378 , ALA A:381 , HOH A:619 , HOH A:627 , HOH A:634 , HOH A:660 , HOH A:661 , HOH A:718 , HOH A:769 , HOH A:815 , HOH A:879	binding site for residue FAD A 501
02	AC2	SOFTWARE	SER A:58 , GLU A:67 , HIS A:69 , PRO A:209 , GLY A:212 , TYR A:213 , HIS A:309	binding site for residue NO3 A 502
03	AC3	SOFTWARE	ARG A:132	binding site for residue NO3 A 503
04	AC4	SOFTWARE	ARG A:82 , HOH A:801 , HOH A:849	binding site for residue SO4 A 504
05	AC5	SOFTWARE	ARG A:323	binding site for residue NO3 A 505
06	AC6	SOFTWARE	GLU A:164 , LYS A:168 , HIS A:169 , HOH A:688	binding site for residue SO4 A 506
07	AC7	SOFTWARE	GLU A:33 , THR A:37 , PHE A:90 , HOH A:725	binding site for residue NO3 A 507
08	AC8	SOFTWARE	PHE B:111 , PHE B:150 , PHE B:166 , ILE B:167 , TYR B:170 , THR B:171 , TRP B:175 , ARG B:189 , LEU B:190 , TYR B:200 , ASN B:291 , ASN B:293 , ARG B:301 , TYR B:337 , TYR B:375 , HOH B:635 , HOH B:684 , HOH B:696 , HOH B:734 , HOH B:755 , HOH B:786 , HOH B:814 , HOH B:834 , HOH B:847	binding site for residue UDP B 501
09	AC9	SOFTWARE	VAL B:22 , GLY B:23 , GLY B:25 , PHE B:26 , PHE B:27 , ILE B:46 , GLU B:47 , ARG B:48 , ARG B:49 , GLY B:54 , ASN B:55 , TYR B:71 , ALA B:73 , HIS B:74 , LEU B:75 , THR B:232 , ASP B:233 , TRP B:234 , PHE B:235 , THR B:253 , GLY B:254 , ARG B:258 , LEU B:272 , TYR B:336 , TYR B:337 , GLY B:368 , ARG B:369 , LEU B:370 , LEU B:376 , ASP B:377 , MET B:378 , ALA B:381 , HOH B:603 , HOH B:604 , HOH B:606 , HOH B:609 , HOH B:618 , HOH B:668 , HOH B:698 , HOH B:753	binding site for residue FAD B 502
10	AD1	SOFTWARE	SER B:58 , GLU B:67 , HIS B:69 , PRO B:209 , GLY B:212 , TYR B:213 , HIS B:309	binding site for residue NO3 B 503
11	AD2	SOFTWARE	ARG B:132	binding site for residue NO3 B 504
12	AD3	SOFTWARE	MET B:103 , HIS B:104 , ASN B:105 , GLY B:106 , ASP B:294 , ASP B:296 , HOH B:792	binding site for residue NO3 B 505
13	AD4	SOFTWARE	LYS A:180 , ARG B:354	binding site for residue SO4 B 506
14	AD5	SOFTWARE	PRO B:183 , ALA B:184 , SER B:185 , ARG B:345 , HOH B:601	binding site for residue SO4 B 507
15	AD6	SOFTWARE	LYS B:81 , ARG B:88 , HOH B:633	binding site for residue SO4 B 508
16	AD7	SOFTWARE	ARG B:124 , HOH B:607 , HOH B:795 , HOH B:803	binding site for residue SO4 B 509

(no "SS Bond" information available for 5EQD)

Asymmetric Unit

No.	Residues
1	Phe A:111	-	Pro A:112
2	Phe B:111	-	Pro B:112

(no "SAP(SNP)/Variant" information available for 5EQD)

(no "PROSITE Motif" information available for 5EQD)

(no "Exon" information available for 5EQD)

Asymmetric 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
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Chain A from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhhhh..eeee......hhhhh.ee......ee.......eee.hhhhhhhhh...........eeeee..eeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.................eee....hhhhhhhhhh....eeee...hhhhhhhhhhhhh....eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhhh.........eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eqd A  14 TGNFDLFVVGSGFFGLTIAERAATQLGKRVLVIERRPHIGGNAYSEPEPETGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTGYQHRVFAMHNGQAYQFPMGLGLVSQFFGRYFSPDEARALIAEQASEIDTKDAKNFEEKAISLVGRPLYEAFIKHYTAKQWQTDPKDLPASNITRLPVRYTFDNRYFNDTYEGLPVEGYTKWLENMAADERIEVRLDTDWFDVRDDLRAANPDAPVVYTGPLDRYFDYAEGRLGWRTLDFELEVLETGDFQGTPVMNYNDLDVPYTRIHEFRHFHPERTYPTDKTVIMREYSRFADNDDEPYYPINTEADRAVLAAYRARAKAETASAKVLFGGRLGTYQYLDMHMAIASALSMFDNVLAPHLSEGASLVT 405
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403

Chain B from PDB  Type:PROTEIN  Length:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhhh..eeee......hhhh.eee......eee......eee.hhhhhhhhh...........eeeee..eeeee..hhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..............eee....hhhhhhhhhh....eeee...hhhhhhhhhhhhh....eee..hhhhhh........eeeeeeeeeee.........eeee........eeee.hhhh.........eeeeeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eqd B  15 GNFDLFVVGSGFFGLTIAERAATQLGKRVLVIERRPHIGGNAYSEPEPETGIEVHKYGAHLFHTSNKRVWDYVRQFTDFTGYQHRVFAMHNGQAYQFPMGLGLVSQFFGRYFSPDEARALIAEQASEIDTKDAKNFEEKAISLVGRPLYEAFIKHYTAKQWQTDPKDLPASNITRLPVRYTFDNRYFNDTYEGLPVEGYTKWLENMAADERIEVRLDTDWFDVRDDLRAANPDAPVVYTGPLDRYFDYAEGRLGWRTLDFELEVLETGDFQGTPVMNYNDLDVPYTRIHEFRHFHPERTYPTDKTVIMREYSRFADNDDEPYYPINTEADRAVLAAYRARAKAETASAKVLFGGRLGTYQYLDMHMAIASALSMFDNVLAPHLSEGASLVT 405
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404

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 '\|'

(no "SCOP Domain" information available for 5EQD)

(no "CATH Domain" information available for 5EQD)

(no "Pfam Domain" information available for 5EQD)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Phe A:111 - Pro A:112	[ RasMol ]
		Phe B:111 - Pro B:112	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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