Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6ED7

Crystal structure of 7,8-diaminopelargonic acid synthase bound to inhibitor MAC13772

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
A	0005737	cellular_component	cytoplasm
A	0008483	molecular_function	transaminase activity
A	0009102	biological_process	biotin biosynthetic process
A	0030170	molecular_function	pyridoxal phosphate binding
A	0042803	molecular_function	protein homodimerization activity
B	0003824	molecular_function	catalytic activity
B	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
B	0005737	cellular_component	cytoplasm
B	0008483	molecular_function	transaminase activity
B	0009102	biological_process	biotin biosynthetic process
B	0030170	molecular_function	pyridoxal phosphate binding
B	0042803	molecular_function	protein homodimerization activity
C	0003824	molecular_function	catalytic activity
C	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
C	0005737	cellular_component	cytoplasm
C	0008483	molecular_function	transaminase activity
C	0009102	biological_process	biotin biosynthetic process
C	0030170	molecular_function	pyridoxal phosphate binding
C	0042803	molecular_function	protein homodimerization activity
D	0003824	molecular_function	catalytic activity
D	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
D	0005737	cellular_component	cytoplasm
D	0008483	molecular_function	transaminase activity
D	0009102	biological_process	biotin biosynthetic process
D	0030170	molecular_function	pyridoxal phosphate binding
D	0042803	molecular_function	protein homodimerization activity
E	0003824	molecular_function	catalytic activity
E	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
E	0005737	cellular_component	cytoplasm
E	0008483	molecular_function	transaminase activity
E	0009102	biological_process	biotin biosynthetic process
E	0030170	molecular_function	pyridoxal phosphate binding
E	0042803	molecular_function	protein homodimerization activity
F	0003824	molecular_function	catalytic activity
F	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
F	0005737	cellular_component	cytoplasm
F	0008483	molecular_function	transaminase activity
F	0009102	biological_process	biotin biosynthetic process
F	0030170	molecular_function	pyridoxal phosphate binding
F	0042803	molecular_function	protein homodimerization activity
G	0003824	molecular_function	catalytic activity
G	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
G	0005737	cellular_component	cytoplasm
G	0008483	molecular_function	transaminase activity
G	0009102	biological_process	biotin biosynthetic process
G	0030170	molecular_function	pyridoxal phosphate binding
G	0042803	molecular_function	protein homodimerization activity
H	0003824	molecular_function	catalytic activity
H	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
H	0005737	cellular_component	cytoplasm
H	0008483	molecular_function	transaminase activity
H	0009102	biological_process	biotin biosynthetic process
H	0030170	molecular_function	pyridoxal phosphate binding
H	0042803	molecular_function	protein homodimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	binding site for residue J4J A 603

Chain	Residue
A	TYR17
B	GLY307
A	TRP52
A	TYR144
A	ASP147
A	ARG391
A	PHE393
A	J4J602
A	HOH741
B	GLY81

site_id	AC2
Number of Residues	10
Details	binding site for residue J4J B 603

Chain	Residue
A	GLY307
B	PRO16
B	TYR17
B	TRP52
B	TYR144
B	ASP147
B	ARG391
B	PHE393
B	J4J602
B	HOH749

site_id	AC3
Number of Residues	10
Details	binding site for residue J4J C 603

Chain	Residue
C	PRO16
C	TYR17
C	TRP52
C	TYR144
C	ASP147
C	ARG391
C	PHE393
C	J4J602
C	HOH747
D	GLY307

site_id	AC4
Number of Residues	8
Details	binding site for residue J4J D 603

Chain	Residue
C	GLY307
D	TYR17
D	TYR144
D	ASP147
D	ARG391
D	PHE393
D	J4J602
D	HOH761

site_id	AC5
Number of Residues	10
Details	binding site for residue J4J E 603

Chain	Residue
E	TYR17
E	TRP52
E	TYR144
E	ASP147
E	ARG391
E	PHE393
E	J4J602
E	HOH734
F	GLY81
F	GLY307

site_id	AC6
Number of Residues	9
Details	binding site for residue J4J F 603

Chain	Residue
E	GLY307
F	PRO16
F	TYR17
F	TRP52
F	TYR144
F	ASP147
F	ARG391
F	PHE393
F	J4J602

site_id	AC7
Number of Residues	10
Details	binding site for residue J4J G 602

Chain	Residue
G	PRO16
G	TYR17
G	TRP52
G	TYR144
G	ASP147
G	ARG391
G	PHE393
G	J4J603
H	GLY81
H	GLY307

site_id	AC8
Number of Residues	10
Details	binding site for residue J4J H 603

Chain	Residue
G	GLY81
G	GLY307
H	PRO16
H	TYR17
H	TRP52
H	TYR144
H	ASP147
H	ARG391
H	PHE393
H	J4J602

site_id	AC9
Number of Residues	21
Details	binding site for residues PLP A 601 and J4J A 602

Chain	Residue
A	TRP52
A	GLY112
A	SER113
A	TYR144
A	HIS145
A	GLY146
A	GLU211
A	ALA217
A	ASP245
A	ILE247
A	LYS274
A	PHE393
A	TYR398
A	J4J603
A	HOH701
A	HOH737
A	HOH744
A	HOH785
B	PRO308
B	THR309
B	HOH718

site_id	AD1
Number of Residues	21
Details	binding site for residues PLP B 601 and J4J B 602

Chain	Residue
A	THR309
A	HOH712
B	TRP52
B	GLY112
B	SER113
B	TYR144
B	HIS145
B	GLY146
B	ALA217
B	ASP245
B	ILE247
B	LYS274
B	PHE393
B	TYR398
B	J4J603
B	HOH709
B	HOH711
B	HOH714
B	HOH767
B	HOH779
A	PRO308

site_id	AD2
Number of Residues	19
Details	binding site for residues PLP C 601 and J4J C 602

Chain	Residue
C	TRP52
C	GLY112
C	SER113
C	TYR144
C	HIS145
C	GLY146
C	ALA217
C	ASP245
C	ILE247
C	LYS274
C	PHE393
C	TYR398
C	J4J603
C	HOH710
C	HOH727
C	HOH733
D	PRO308
D	THR309
D	HOH730

site_id	AD3
Number of Residues	23
Details	binding site for residues PLP D 601 and J4J D 602

Chain	Residue
C	PRO308
C	THR309
C	HOH736
D	TRP52
D	GLY112
D	SER113
D	TYR144
D	HIS145
D	GLY146
D	ALA217
D	ASP245
D	ILE247
D	ALA248
D	LYS274
D	PHE393
D	TYR398
D	J4J603
D	HOH701
D	HOH728
D	HOH734
D	HOH738
D	HOH744
D	HOH752

site_id	AD4
Number of Residues	20
Details	binding site for residues PLP E 601 and J4J E 602

Chain	Residue
E	TRP52
E	SER111
E	GLY112
E	SER113
E	TYR144
E	HIS145
E	GLU211
E	ALA217
E	ASP245
E	ILE247
E	LYS274
E	PHE393
E	TYR398
E	J4J603
E	HOH729
E	HOH754
E	HOH759
E	HOH773
F	PRO308
F	THR309

site_id	AD5
Number of Residues	22
Details	binding site for residues PLP F 601 and J4J F 602

Chain	Residue
E	PRO308
E	THR309
E	HOH730
F	TRP52
F	GLY112
F	SER113
F	TYR144
F	HIS145
F	GLY146
F	ALA217
F	ASP245
F	ILE247
F	LYS274
F	PHE393
F	TYR398
F	J4J603
F	HOH742
F	HOH743
F	HOH746
F	HOH755
F	HOH756
F	HOH769

site_id	AD6
Number of Residues	22
Details	binding site for residues PLP G 601 and J4J G 603

Chain	Residue
G	TRP52
G	TRP53
G	GLY112
G	SER113
G	TYR144
G	HIS145
G	GLY146
G	ALA217
G	ASP245
G	ILE247
G	ALA248
G	LYS274
G	PHE393
G	TYR398
G	J4J602
G	HOH706
G	HOH723
G	HOH737
G	HOH740
H	PRO308
H	THR309
H	HOH738

site_id	AD7
Number of Residues	22
Details	binding site for residues PLP H 601 and J4J H 602

Chain	Residue
G	PRO308
G	THR309
H	TRP52
H	GLY112
H	SER113
H	TYR144
H	HIS145
H	GLY146
H	GLU211
H	ALA217
H	ASP245
H	ILE247
H	ALA248
H	LYS274
H	PHE393
H	TYR398
H	J4J603
H	HOH710
H	HOH723
H	HOH734
H	HOH736
H	HOH761

Functional Information from PROSITE/UniProt

site_id	PS00600
Number of Residues	38
Details	AA_TRANSFER_CLASS_3 Aminotransferases class-III pyridoxal-phosphate attachment site. LIaDEIat.GFgRtGklfacehaeiap....DILclGKaltGG

Chain	Residue	Details
A	LEU242-GLY279

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	16
Details	BINDING: BINDING => ECO:0000269\|PubMed:10452893, ECO:0000269\|PubMed:12218056, ECO:0007744\|PDB:1MLY, ECO:0007744\|PDB:1QJ3

Chain	Residue	Details
A	TRP52
E	LYS274
F	TRP52
F	LYS274
G	TRP52
G	LYS274
H	TRP52
H	LYS274
A	LYS274
B	TRP52
B	LYS274
C	TRP52
C	LYS274
D	TRP52
D	LYS274
E	TRP52

site_id	SWS_FT_FI2
Number of Residues	16
Details	BINDING: BINDING => ECO:0000269\|PubMed:10452893, ECO:0000269\|PubMed:12379100, ECO:0000269\|PubMed:14756557, ECO:0007744\|PDB:1DTY, ECO:0007744\|PDB:1MGV, ECO:0007744\|PDB:1QJ3, ECO:0007744\|PDB:1QJ5, ECO:0007744\|PDB:1S07

Chain	Residue	Details
A	GLY112
E	PRO308
F	GLY112
F	PRO308
G	GLY112
G	PRO308
H	GLY112
H	PRO308
A	PRO308
B	GLY112
B	PRO308
C	GLY112
C	PRO308
D	GLY112
D	PRO308
E	GLY112

site_id	SWS_FT_FI3
Number of Residues	8
Details	BINDING: BINDING => ECO:0000305\|PubMed:10452893

Chain	Residue	Details
A	TYR144
B	TYR144
C	TYR144
D	TYR144
E	TYR144
F	TYR144
G	TYR144
H	TYR144

site_id	SWS_FT_FI4
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:10452893, ECO:0000269\|PubMed:12379100, ECO:0000269\|PubMed:14756557, ECO:0007744\|PDB:1MGV, ECO:0007744\|PDB:1QJ3, ECO:0007744\|PDB:1QJ5, ECO:0007744\|PDB:1S07

Chain	Residue	Details
A	ASP245
B	ASP245
C	ASP245
D	ASP245
E	ASP245
F	ASP245
G	ASP245
H	ASP245

site_id	SWS_FT_FI5
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:10452893, ECO:0007744\|PDB:1QJ3

Chain	Residue	Details
A	GLY307
B	GLY307
C	GLY307
D	GLY307
E	GLY307
F	GLY307
G	GLY307
H	GLY307

site_id	SWS_FT_FI6
Number of Residues	8
Details	BINDING: BINDING => ECO:0000269\|PubMed:10452893, ECO:0000269\|PubMed:12218056, ECO:0007744\|PDB:1MLY, ECO:0007744\|PDB:1MLZ, ECO:0007744\|PDB:1QJ3

Chain	Residue	Details
A	ARG391
B	ARG391
C	ARG391
D	ARG391
E	ARG391
F	ARG391
G	ARG391
H	ARG391

site_id	SWS_FT_FI7
Number of Residues	8
Details	SITE: Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAM => ECO:0000305

Chain	Residue	Details
A	TYR17
B	TYR17
C	TYR17
D	TYR17
E	TYR17
F	TYR17
G	TYR17
H	TYR17

site_id	SWS_FT_FI8
Number of Residues	8
Details	MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269\|PubMed:12379100, ECO:0000269\|PubMed:14756557, ECO:0007744\|PDB:1DTY, ECO:0007744\|PDB:1MGV, ECO:0007744\|PDB:1QJ3, ECO:0007744\|PDB:1QJ5, ECO:0007744\|PDB:1S06, ECO:0007744\|PDB:1S08, ECO:0007744\|PDB:1S09, ECO:0007744\|PDB:1S0A

Chain	Residue	Details
A	LYS274
B	LYS274
C	LYS274
D	LYS274
E	LYS274
F	LYS274
G	LYS274
H	LYS274

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
A	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
A	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
A	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
A	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA2
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
B	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
B	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
B	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
B	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA3
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
C	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
C	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
C	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
C	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA4
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
D	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
D	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
D	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
D	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA5
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
E	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
E	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
E	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
E	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA6
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
F	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
F	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
F	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
F	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA7
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
G	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
G	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
G	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
G	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

site_id	MCSA8
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
H	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
H	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
H	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
H	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)