3DAQ - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS

Authors :   R. C. J. Dobson, B. R. Burgess, G. B. Jameson, J. A. Gerrard, M. W. Parker, M. A. Perugini

Date :   29 May 08 (Deposition) - 05 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

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

Keywords :   Dihydrodipicolinate Synthase, Lysine Biosynthesis, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Schiff Base (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. R. Burgess, R. C. J. Dobson, M. F. Bailey, S. C. Atkinson, M. D. W. Griffin, G. B. Jameson, M. W. Parker, J. A. Gerrard, M. A. Perugini
Structure And Evolution Of A Novel Dimeric Enzyme From A Clinically-Important Bacterial Pathogen.
J. Biol. Chem. 2008
PubMed-ID: 18684709 | Reference-DOI: 10.1074/JBC.M804231200

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
	Chains	:	A, B, C, D
	EC Number	:	4.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-293
	Gene	:	DAPA, SAR1407
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	282458
	Synonym	:	DHDPS

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	GOL	9	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	5	Ligand/Ion	GLYCEROL

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR D:13 , PRO D:15 , HIS D:29 , HOH D:340 , HOH D:372	BINDING SITE FOR RESIDUE CL D 1
02	AC2	SOFTWARE	THR C:13 , PRO C:15 , HIS C:29 , HOH C:341 , HOH C:365	BINDING SITE FOR RESIDUE CL C 294
03	AC3	SOFTWARE	THR A:13 , PRO A:15 , HIS A:29 , HOH A:327 , HOH A:340	BINDING SITE FOR RESIDUE CL A 294
04	AC4	SOFTWARE	THR B:13 , PRO B:15 , HIS B:29 , HOH B:337 , HOH B:343	BINDING SITE FOR RESIDUE CL B 294
05	AC5	SOFTWARE	TYR D:135 , ARG D:140 , LYS D:163 , ALA D:165 , GLY D:189 , ASN D:249 , HOH D:389 , HOH D:436 , HOH D:476 , HOH D:731	BINDING SITE FOR RESIDUE GOL D 294
06	AC6	SOFTWARE	TYR B:135 , ARG B:140 , LYS B:163 , GLY B:189 , ASN B:249 , HOH B:385 , HOH B:431 , HOH B:493	BINDING SITE FOR RESIDUE GOL B 295
07	AC7	SOFTWARE	TYR C:135 , ARG C:140 , LYS C:163 , ALA C:165 , GLY C:189 , ASN C:249 , HOH C:373 , HOH C:396	BINDING SITE FOR RESIDUE GOL C 295
08	AC8	SOFTWARE	TYR A:135 , ARG A:140 , LYS A:163 , ALA A:165 , GLY A:189 , ASN A:249 , HOH A:389 , HOH A:447 , HOH A:484 , HOH A:656	BINDING SITE FOR RESIDUE GOL A 295
09	AC9	SOFTWARE	ASN C:44 , GLY C:45 , THR C:46 , SER C:50 , GLY C:78 , GLY C:80 , MET C:103 , LEU C:104 , ILE C:105 , TYR D:109	BINDING SITE FOR RESIDUE GOL C 296
10	BC1	SOFTWARE	ASP B:168 , GLU B:170 , TYR B:171 , GLN C:199 , GLN C:224 , GLY C:227 , LEU C:228 , ASP C:229 , HOH C:374	BINDING SITE FOR RESIDUE GOL C 297
11	BC2	SOFTWARE	TYR C:109 , ASN D:44 , GLY D:45 , THR D:46 , SER D:50 , GLY D:80 , MET D:103 , LEU D:104 , ILE D:105	BINDING SITE FOR RESIDUE GOL D 295
12	BC3	SOFTWARE	ASN A:44 , GLY A:45 , THR A:46 , SER A:50 , GLY A:78 , GLY A:80 , MET A:103 , LEU A:104 , ILE A:105 , HOH A:732 , TYR B:109	BINDING SITE FOR RESIDUE GOL A 296
13	BC4	SOFTWARE	TYR A:109 , ASN B:44 , GLY B:45 , THR B:46 , SER B:50 , GLY B:78 , GLY B:80 , MET B:103 , LEU B:104 , ILE B:105 , TYR B:135	BINDING SITE FOR RESIDUE GOL B 296

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

Asymmetric Unit

No.	Residues
1	Asn A:249	-	Pro A:250
2	Leu A:269	-	Pro A:270
3	Asn B:249	-	Pro B:250
4	Leu B:269	-	Pro B:270
5	Asn C:249	-	Pro C:250
6	Leu C:269	-	Pro C:270
7	Asn D:249	-	Pro D:250
8	Leu D:269	-	Pro D:270

(no "SAP(SNP)/Variant" information available for 3DAQ)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	DAPA_STAAR	135-165	4	A:135-165 B:135-165 C:135-165 D:135-165

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	DAPA_STAAR	135-165	2	A:135-165 B:135-165 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	DAPA_STAAR	135-165	2	- - C:135-165 D:135-165

(no "Exon" information available for 3DAQ)

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:292
 aligned with DAPA_STAAR | Q6GH13 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:292
                                    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  
           DAPA_STAAR     2 THLFEGVGVALTTPFTNNKVNLEALKAHVNFLLENNAQAIIVNGTTAESPTLTTDEKELILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLREAYDTFKAGE 293
               SCOP domains d3daqa_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3daqA00 A:2-293 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhh.......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhh..............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: A:135-165        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3daq A   2 THLFEGVGVALTTPFTNNKVNLEALKAHVNFLLENNAQAIIVNGTTAESPTLTTDEKELILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLREAYDTFKAGE 293
                                    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

Chain B from PDB  Type:PROTEIN  Length:292
 aligned with DAPA_STAAR | Q6GH13 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:292
                                    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  
           DAPA_STAAR     2 THLFEGVGVALTTPFTNNKVNLEALKAHVNFLLENNAQAIIVNGTTAESPTLTTDEKELILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLREAYDTFKAGE 293
               SCOP domains d3daqb_ B: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3daqB00 B:2-293 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhh.......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhh..............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: B:135-165        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3daq B   2 THLFEGVGVALTTPFTNNKVNLEALKAHVNFLLENNAQAIIVNGTTAESPTLTTDEKELILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLREAYDTFKAGE 293
                                    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

Chain C from PDB  Type:PROTEIN  Length:292
 aligned with DAPA_STAAR | Q6GH13 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:292
                                    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  
           DAPA_STAAR     2 THLFEGVGVALTTPFTNNKVNLEALKAHVNFLLENNAQAIIVNGTTAESPTLTTDEKELILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLREAYDTFKAGE 293
               SCOP domains d3daqc_ C: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3daqC00 C:2-293 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhh.......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhh..............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: C:135-165        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3daq C   2 THLFEGVGVALTTPFTNNKVNLEALKAHVNFLLENNAQAIIVNGTTAESPTLTTDEKELILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLREAYDTFKAGE 293
                                    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

Chain D from PDB  Type:PROTEIN  Length:292
 aligned with DAPA_STAAR | Q6GH13 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:292
                                    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  
           DAPA_STAAR     2 THLFEGVGVALTTPFTNNKVNLEALKAHVNFLLENNAQAIIVNGTTAESPTLTTDEKELILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLREAYDTFKAGE 293
               SCOP domains d3daqd_ D: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3daqD00 D:2-293 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhh.......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhh..............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: D:135-165        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3daq D   2 THLFEGVGVALTTPFTNNKVNLEALKAHVNFLLENNAQAIIVNGTTAESPTLTTDEKELILKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHFEAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDTNSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSGLDIQDQFKPIGTLLSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLREAYDTFKAGE 293
                                    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

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Staphylococcus aureus [TaxId: 282458] (1)

1a	d3daqa_	A:
1b	d3daqb_	B:
1c	d3daqc_	C:
1d	d3daqd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Staphylococcus aureus. Organism_taxid: 282458. (1)

1a	3daqA00	A:2-293
1b	3daqB00	B:2-293
1c	3daqC00	C:2-293
1d	3daqD00	D:2-293

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DAPA_STAAR | Q6GH13)

molecular function
	GO:0008840	4-hydroxy-tetrahydrodipicolinate synthase	Catalysis of the reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019877	diaminopimelate biosynthetic process	The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0009089	lysine biosynthetic process via diaminopimelate	The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:249 - Pro A:250	[ RasMol ]
		Asn B:249 - Pro B:250	[ RasMol ]
		Asn C:249 - Pro C:250	[ RasMol ]
		Asn D:249 - Pro D:250	[ RasMol ]
		Leu A:269 - Pro A:270	[ RasMol ]
		Leu B:269 - Pro B:270	[ RasMol ]
		Leu C:269 - Pro C:270	[ RasMol ]
		Leu D:269 - Pro D:270	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3daq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	DAPA_STAAR \| Q6GH13
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.2.1.52
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	DAPA_STAAR \| Q6GH13
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3DAQ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File