5KKB - JenaLib

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Title :   STRUCTURE OF MOUSE GOLGI ALPHA-1,2-MANNOSIDASE IA AND MAN9GLCNAC2-PA COMPLEX

Authors :   Y. Xiang, K. W. Moremen

Date :   21 Jun 16 (Deposition) - 07 Dec 16 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

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

Keywords :   Alpha/Alpha Barrel, Golgi Apparatus, Deglycosylation, Glycan Substrate Analog, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Xiang, K. Karaveg, K. W. Moremen
Substrate Recognition And Catalysis By Gh47 Alpha-Mannosidases Involved In Asn-Linked Glycan Maturation In The Mammalian Secretory Pathway.
Proc. Natl. Acad. Sci. V. 113 E7890 2016 U. S. A.
PubMed-ID: 27856750 | Reference-DOI: 10.1073/PNAS.1611213113

Molecule 1 - MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE IA
	Chains	:	A, B
	EC Number	:	3.2.1.113
	Engineered	:	YES
	Expression System	:	KOMAGATAELLA PASTORIS
	Expression System Taxid	:	4922
	Gene	:	MAN1A1, MAN1A
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MAN(9)-ALPHA-MANNOSIDASE,MAN9-MANNOSIDASE,MANNOSIDASE ALPHA CLASS 1A MEMBER 1,PROCESSING ALPHA-1,2-MANNOSIDASE IA,ALPHA-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 25)

No.	Name	Count	Type	Full Name
1	1PS	2	Ligand/Ion	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2	BMA	2	Ligand/Ion	BETA-D-MANNOSE
3	BU1	1	Ligand/Ion	1,4-BUTANEDIOL
4	LA	2	Ligand/Ion	LANTHANUM (III) ION
5	MAN	14	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (4, 11)

No.	Name	Count	Type	Full Name
1	1PS	1	Ligand/Ion	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	BU1	-1	Ligand/Ion	1,4-BUTANEDIOL
4	LA	-1	Ligand/Ion	LANTHANUM (III) ION
5	MAN	7	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (5, 12)

No.	Name	Count	Type	Full Name
1	1PS	1	Ligand/Ion	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	BU1	1	Ligand/Ion	1,4-BUTANEDIOL
4	LA	-1	Ligand/Ion	LANTHANUM (III) ION
5	MAN	7	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:635 , MAN A:709 , HOH A:808 , HOH A:827 , HOH A:927 , HOH A:1003 , HOH A:1029	binding site for residue LA A 711
2	AC2	SOFTWARE	LEU A:315 , PRO A:316 , HIS A:319 , VAL A:370 , LYS A:374 , HOH A:803 , HOH A:845 , HOH A:901 , HOH B:1040	binding site for residue 1PS A 712
3	AC3	SOFTWARE	HOH A:1034 , VAL B:312 , LEU B:315 , PRO B:316 , HIS B:319 , HOH B:943	binding site for residue 1PS B 711
4	AC4	SOFTWARE	THR B:635 , MAN B:709 , HOH B:805 , HOH B:835 , HOH B:898 , HOH B:1015 , HOH B:1026	binding site for residue LA B 712
5	AC5	SOFTWARE	LYS B:332 , ASP B:622 , ASP B:623 , ASP B:624 , HOH B:823	binding site for residue BU1 B 713
6	AC6	SOFTWARE	ASN A:515 , LYS A:520	binding site for Mono-Saccharide NAG A 710 bound to ASN A 515
7	AC7	SOFTWARE	ASN B:515 , LYS B:520 , HOH B:802	binding site for Mono-Saccharide NAG B 710 bound to ASN B 515
8	AC8	SOFTWARE	HIS A:230 , SER A:232 , SER A:233 , LEU A:234 , PHE A:281 , ARG A:286 , TRP A:339 , TRP A:341 , ILE A:348 , ALA A:350 , GLU A:351 , GLY A:412 , LEU A:413 , ASP A:415 , LEU A:476 , ASN A:540 , ARG A:547 , PRO A:548 , GLU A:549 , PHE A:607 , GLU A:611 , THR A:635 , GLU A:636 , LA A:711 , HOH A:806 , HOH A:809 , HOH A:818 , HOH A:825 , HOH A:832 , HOH A:841 , HOH A:849 , HOH A:872 , HOH A:884 , HOH A:886 , HOH A:936 , HOH A:944 , HOH A:961 , HOH A:980 , HOH A:1024	binding site for Poly-Saccharide residues BMA A 701 through MAN A 709
9	AC9	SOFTWARE	HIS A:230 , SER A:232 , SER A:233 , LEU A:234 , PHE A:281 , ARG A:286 , TRP A:339 , TRP A:341 , ILE A:348 , ALA A:350 , GLU A:351 , GLY A:412 , LEU A:413 , ASP A:415 , LEU A:476 , ASN A:540 , ARG A:547 , PRO A:548 , GLU A:549 , PHE A:607 , GLU A:611 , THR A:635 , GLU A:636 , LA A:711 , HOH A:806 , HOH A:809 , HOH A:818 , HOH A:825 , HOH A:832 , HOH A:841 , HOH A:849 , HOH A:872 , HOH A:884 , HOH A:886 , HOH A:936 , HOH A:944 , HOH A:961 , HOH A:980 , HOH A:1024 , HIS B:230 , SER B:232 , SER B:233 , LEU B:234 , PHE B:281 , ILE B:285 , ARG B:286 , TRP B:339 , TRP B:341 , ILE B:348 , ALA B:350 , GLU B:351 , GLY B:412 , LEU B:413 , ASP B:415 , LEU B:476 , ARG B:547 , PRO B:548 , GLU B:549 , PHE B:607 , GLU B:611 , THR B:635 , GLU B:636 , LA B:712 , HOH B:811 , HOH B:814 , HOH B:818 , HOH B:843 , HOH B:860 , HOH B:862 , HOH B:869 , HOH B:874 , HOH B:897 , HOH B:915 , HOH B:917 , HOH B:931 , HOH B:941 , HOH B:951 , HOH B:970	binding site for Poly-Saccharide residues BMA B 701 through MAN B 709

Asymmetric Unit

No.	Residues
1	A:478	-	A:510
2	B:478	-	B:510

Asymmetric Unit

No.	Residues
1	Glu A:493	-	Ala A:494
2	Gly A:530	-	Gly A:531
3	Ala B:491	-	Pro B:492
4	Glu B:493	-	Ala B:494
5	Gly B:531	-	Val B:532

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

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

(no "Exon" information available for 5KKB)

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
	(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:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eee.hhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee....eee....hhhhheehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhh...ee..........ee.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhheee.....eee.eee..eee.eee.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh........eeee....eee..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee.................hhhhhhhhhhhhhhhh..........eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kkb A 176 VDFLPPVGVENREPADATIREKRAKIKEMMTHAWNNYKRYAWGLNELKPISKEGHSSSLFGNIKGATIVDALDTLFIMGMKTEFQEAKSWIKKYLDFNVNAEVSVFEVNIRFVGGLLSAYYLSGEEIFRKKAVELGVKLLPAFHTPSGIPWALLNMKSGIGRNWPWASGGSSILAEFGTLHLEFMHLSHLSGDPVFAEKVMKIRTVLNKLDKPEGLYPNYLNPSSGQWGQHHVSVGGLGDSFYEYLLKAWLMSDKTDLEAKKMYFDAVQAIETHLIRKSSGGLTYIAEWKGGLLEHKMGHLTCFAGGMFALGADGAPEARAQHYLELGAEIARTCHESYNRTYVKLGPEAFRFDGGVEAIATRQNEKYYILRPEVIETYMYMWRLTHDPKYRTWAWEAVEALESHCRVNGGYSGLRDVYIARESYDDVQQSFFLAETLKYLYLIFSDDDLLPLEHWIFNTEAHPFPILR 644
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635

Chain B from PDB  Type:PROTEIN  Length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eee.hhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee....eee....hhhhheehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhh...ee..........ee.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhheee.....eee.eee..eee.eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh........eee..........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee.................hhhhhhhhhhhhhhhh..........eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kkb B 176 VDFLPPVGVENREPADATIREKRAKIKEMMTHAWNNYKRYAWGLNELKPISKEGHSSSLFGNIKGATIVDALDTLFIMGMKTEFQEAKSWIKKYLDFNVNAEVSVFEVNIRFVGGLLSAYYLSGEEIFRKKAVELGVKLLPAFHTPSGIPWALLNMKSGIGRNWPWASGGSSILAEFGTLHLEFMHLSHLSGDPVFAEKVMKIRTVLNKLDKPEGLYPNYLNPSSGQWGQHHVSVGGLGDSFYEYLLKAWLMSDKTDLEAKKMYFDAVQAIETHLIRKSSGGLTYIAEWKGGLLEHKMGHLTCFAGGMFALGADGAPEARAQHYLELGAEIARTCHESYNRTYVKLGPEAFRFDGGVEAIATRQNEKYYILRPEVIETYMYMWRLTHDPKYRTWAWEAVEALESHCRVNGGYSGLRDVYIARESYDDVQQSFFLAETLKYLYLIFSDDDLLPLEHWIFNTEAHPFPILR 644
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635

Legend:		→ Mismatch	(orange background)
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	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 5KKB)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala B:491 - Pro B:492	[ RasMol ]
		Glu A:493 - Ala A:494	[ RasMol ]
		Glu B:493 - Ala B:494	[ RasMol ]
		Gly A:530 - Gly A:531	[ RasMol ]
		Gly B:531 - Val B:532	[ RasMol ]

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	5kkb
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	3.2.1.113
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(no "Related Entries Specified in the PDB File" available for 5KKB)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 25)

Sites (9, 9)

SS Bonds (2, 2)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (16, 16)

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