Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6IKM

Crystal structure of SpuE-Spermidine in complex with ScFv5

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005615	cellular_component	extracellular space
A	0015846	biological_process	polyamine transport
A	0015847	biological_process	putrescine transport
A	0019808	molecular_function	polyamine binding
A	0019809	molecular_function	spermidine binding
A	0019810	molecular_function	putrescine binding
A	0030288	cellular_component	outer membrane-bounded periplasmic space
A	0042597	cellular_component	periplasmic space
B	0005615	cellular_component	extracellular space
B	0015846	biological_process	polyamine transport
B	0015847	biological_process	putrescine transport
B	0019808	molecular_function	polyamine binding
B	0019809	molecular_function	spermidine binding
B	0019810	molecular_function	putrescine binding
B	0030288	cellular_component	outer membrane-bounded periplasmic space
B	0042597	cellular_component	periplasmic space
C	0005615	cellular_component	extracellular space
C	0015846	biological_process	polyamine transport
C	0015847	biological_process	putrescine transport
C	0019808	molecular_function	polyamine binding
C	0019809	molecular_function	spermidine binding
C	0019810	molecular_function	putrescine binding
C	0030288	cellular_component	outer membrane-bounded periplasmic space
C	0042597	cellular_component	periplasmic space
D	0005615	cellular_component	extracellular space
D	0015846	biological_process	polyamine transport
D	0015847	biological_process	putrescine transport
D	0019808	molecular_function	polyamine binding
D	0019809	molecular_function	spermidine binding
D	0019810	molecular_function	putrescine binding
D	0030288	cellular_component	outer membrane-bounded periplasmic space
D	0042597	cellular_component	periplasmic space
E	0005615	cellular_component	extracellular space
E	0015846	biological_process	polyamine transport
E	0015847	biological_process	putrescine transport
E	0019808	molecular_function	polyamine binding
E	0019809	molecular_function	spermidine binding
E	0019810	molecular_function	putrescine binding
E	0030288	cellular_component	outer membrane-bounded periplasmic space
E	0042597	cellular_component	periplasmic space
F	0005615	cellular_component	extracellular space
F	0015846	biological_process	polyamine transport
F	0015847	biological_process	putrescine transport
F	0019808	molecular_function	polyamine binding
F	0019809	molecular_function	spermidine binding
F	0019810	molecular_function	putrescine binding
F	0030288	cellular_component	outer membrane-bounded periplasmic space
F	0042597	cellular_component	periplasmic space
G	0005615	cellular_component	extracellular space
G	0015846	biological_process	polyamine transport
G	0015847	biological_process	putrescine transport
G	0019808	molecular_function	polyamine binding
G	0019809	molecular_function	spermidine binding
G	0019810	molecular_function	putrescine binding
G	0030288	cellular_component	outer membrane-bounded periplasmic space
G	0042597	cellular_component	periplasmic space
H	0005615	cellular_component	extracellular space
H	0015846	biological_process	polyamine transport
H	0015847	biological_process	putrescine transport
H	0019808	molecular_function	polyamine binding
H	0019809	molecular_function	spermidine binding
H	0019810	molecular_function	putrescine binding
H	0030288	cellular_component	outer membrane-bounded periplasmic space
H	0042597	cellular_component	periplasmic space
I	0005615	cellular_component	extracellular space
I	0015846	biological_process	polyamine transport
I	0015847	biological_process	putrescine transport
I	0019808	molecular_function	polyamine binding
I	0019809	molecular_function	spermidine binding
I	0019810	molecular_function	putrescine binding
I	0030288	cellular_component	outer membrane-bounded periplasmic space
I	0042597	cellular_component	periplasmic space
J	0005615	cellular_component	extracellular space
J	0015846	biological_process	polyamine transport
J	0015847	biological_process	putrescine transport
J	0019808	molecular_function	polyamine binding
J	0019809	molecular_function	spermidine binding
J	0019810	molecular_function	putrescine binding
J	0030288	cellular_component	outer membrane-bounded periplasmic space
J	0042597	cellular_component	periplasmic space
K	0005615	cellular_component	extracellular space
K	0015846	biological_process	polyamine transport
K	0015847	biological_process	putrescine transport
K	0019808	molecular_function	polyamine binding
K	0019809	molecular_function	spermidine binding
K	0019810	molecular_function	putrescine binding
K	0030288	cellular_component	outer membrane-bounded periplasmic space
K	0042597	cellular_component	periplasmic space
L	0005615	cellular_component	extracellular space
L	0015846	biological_process	polyamine transport
L	0015847	biological_process	putrescine transport
L	0019808	molecular_function	polyamine binding
L	0019809	molecular_function	spermidine binding
L	0019810	molecular_function	putrescine binding
L	0030288	cellular_component	outer membrane-bounded periplasmic space
L	0042597	cellular_component	periplasmic space
M	0005615	cellular_component	extracellular space
M	0015846	biological_process	polyamine transport
M	0015847	biological_process	putrescine transport
M	0019808	molecular_function	polyamine binding
M	0019809	molecular_function	spermidine binding
M	0019810	molecular_function	putrescine binding
M	0030288	cellular_component	outer membrane-bounded periplasmic space
M	0042597	cellular_component	periplasmic space
N	0005615	cellular_component	extracellular space
N	0015846	biological_process	polyamine transport
N	0015847	biological_process	putrescine transport
N	0019808	molecular_function	polyamine binding
N	0019809	molecular_function	spermidine binding
N	0019810	molecular_function	putrescine binding
N	0030288	cellular_component	outer membrane-bounded periplasmic space
N	0042597	cellular_component	periplasmic space
O	0005615	cellular_component	extracellular space
O	0015846	biological_process	polyamine transport
O	0015847	biological_process	putrescine transport
O	0019808	molecular_function	polyamine binding
O	0019809	molecular_function	spermidine binding
O	0019810	molecular_function	putrescine binding
O	0030288	cellular_component	outer membrane-bounded periplasmic space
O	0042597	cellular_component	periplasmic space
P	0005615	cellular_component	extracellular space
P	0015846	biological_process	polyamine transport
P	0015847	biological_process	putrescine transport
P	0019808	molecular_function	polyamine binding
P	0019809	molecular_function	spermidine binding
P	0019810	molecular_function	putrescine binding
P	0030288	cellular_component	outer membrane-bounded periplasmic space
P	0042597	cellular_component	periplasmic space
Q	0005615	cellular_component	extracellular space
Q	0015846	biological_process	polyamine transport
Q	0015847	biological_process	putrescine transport
Q	0019808	molecular_function	polyamine binding
Q	0019809	molecular_function	spermidine binding
Q	0019810	molecular_function	putrescine binding
Q	0030288	cellular_component	outer membrane-bounded periplasmic space
Q	0042597	cellular_component	periplasmic space
R	0005615	cellular_component	extracellular space
R	0015846	biological_process	polyamine transport
R	0015847	biological_process	putrescine transport
R	0019808	molecular_function	polyamine binding
R	0019809	molecular_function	spermidine binding
R	0019810	molecular_function	putrescine binding
R	0030288	cellular_component	outer membrane-bounded periplasmic space
R	0042597	cellular_component	periplasmic space

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue SO4 A 401

Chain	Residue
A	PRO347
A	ALA348
K	ARG352

site_id	AC2
Number of Residues	3
Details	binding site for residue SO4 A 402

Chain	Residue
A	LEU353
A	ARG356
A	ARG360

site_id	AC3
Number of Residues	3
Details	binding site for residue SO4 A 403

Chain	Residue
A	LYS349
A	ARG352
A	ARG356

site_id	AC4
Number of Residues	9
Details	binding site for residue SPD A 404

Chain	Residue
A	TRP34
A	THR35
A	SER82
A	GLU181
A	TYR239
A	ASP242
A	TRP271
A	ASP273
A	TYR309

site_id	AC5
Number of Residues	5
Details	binding site for residue SO4 B 401

Chain	Residue
B	LYS88
B	LEU346
B	PRO347
B	ALA348
G	ARG352

site_id	AC6
Number of Residues	3
Details	binding site for residue SO4 B 402

Chain	Residue
B	LEU353
B	ARG356
B	ARG360

site_id	AC7
Number of Residues	4
Details	binding site for residue SO4 B 403

Chain	Residue
B	ARG352
G	LYS88
G	PRO347
G	ALA348

site_id	AC8
Number of Residues	3
Details	binding site for residue SO4 B 404

Chain	Residue
B	LYS349
B	ARG352
B	ARG356

site_id	AC9
Number of Residues	3
Details	binding site for residue SO4 C 401

Chain	Residue
C	LYS88
C	ALA348
I	ARG352

site_id	AD1
Number of Residues	2
Details	binding site for residue SO4 C 402

Chain	Residue
C	ARG356
C	ARG360

site_id	AD2
Number of Residues	3
Details	binding site for residue SO4 C 403

Chain	Residue
C	LYS349
C	ARG352
C	ARG356

site_id	AD3
Number of Residues	5
Details	binding site for residue SO4 D 401

Chain	Residue
D	LYS88
D	PRO347
D	ALA348
J	LYS349
J	ARG352

site_id	AD4
Number of Residues	3
Details	binding site for residue SO4 D 402

Chain	Residue
D	LEU353
D	ARG356
D	ARG360

site_id	AD5
Number of Residues	3
Details	binding site for residue SO4 D 403

Chain	Residue
D	LYS349
D	ARG352
D	ARG356

site_id	AD6
Number of Residues	9
Details	binding site for residue SPD D 404

Chain	Residue
D	THR35
D	TYR37
D	SER82
D	GLU181
D	TYR239
D	ASP242
D	TRP271
D	ASP273
D	TYR309

site_id	AD7
Number of Residues	6
Details	binding site for residue SO4 E 401

Chain	Residue
E	LYS88
E	LEU346
E	PRO347
E	ALA348
H	LYS349
H	ARG352

site_id	AD8
Number of Residues	3
Details	binding site for residue SO4 E 402

Chain	Residue
E	LEU353
E	ARG356
E	ARG360

site_id	AD9
Number of Residues	3
Details	binding site for residue SO4 E 404

Chain	Residue
E	LYS349
E	ARG352
E	ARG356

site_id	AE1
Number of Residues	5
Details	binding site for residue SO4 F 401

Chain	Residue
F	LYS88
F	LEU346
F	PRO347
F	ALA348
M	ARG352

site_id	AE2
Number of Residues	3
Details	binding site for residue SO4 F 402

Chain	Residue
F	LEU353
F	ARG356
F	ARG360

site_id	AE3
Number of Residues	4
Details	binding site for residue SO4 F 403

Chain	Residue
F	LYS349
F	ARG352
F	ARG356
M	GLN91

site_id	AE4
Number of Residues	12
Details	binding site for residue SPD F 404

Chain	Residue
F	TRP34
F	THR35
F	TYR37
F	ASN62
F	SER82
F	GLU181
F	TYR239
F	ASP242
F	ASN269
F	TRP271
F	ASP273
F	TYR309

site_id	AE5
Number of Residues	3
Details	binding site for residue SO4 G 401

Chain	Residue
G	ARG360
G	LEU353
G	ARG356

site_id	AE6
Number of Residues	4
Details	binding site for residue SO4 G 402

Chain	Residue
B	GLN91
G	LYS349
G	ARG352
G	ARG356

site_id	AE7
Number of Residues	11
Details	binding site for residue SPD G 403

Chain	Residue
G	TRP34
G	THR35
G	TYR37
G	ASN62
G	SER82
G	GLU181
G	TYR239
G	ASP242
G	TRP271
G	ASP273
G	TYR309

site_id	AE8
Number of Residues	3
Details	binding site for residue SO4 H 401

Chain	Residue
H	LEU353
H	ARG356
H	ARG360

site_id	AE9
Number of Residues	12
Details	binding site for residue SPD H 403

Chain	Residue
H	TRP34
H	THR35
H	TYR37
H	ASN62
H	SER82
H	GLU181
H	TYR239
H	ASP242
H	ASN269
H	TRP271
H	ASP273
H	TYR309

site_id	AF1
Number of Residues	2
Details	binding site for residue SO4 I 401

Chain	Residue
I	ARG356
I	ARG360

site_id	AF2
Number of Residues	4
Details	binding site for residue SO4 I 402

Chain	Residue
C	GLN91
I	LYS349
I	ARG352
I	ARG356

site_id	AF3
Number of Residues	4
Details	binding site for residue SO4 I 403

Chain	Residue
C	ARG352
I	LYS88
I	PRO347
I	ALA348

site_id	AF4
Number of Residues	2
Details	binding site for residue SO4 J 401

Chain	Residue
J	ARG356
J	ARG360

site_id	AF5
Number of Residues	4
Details	binding site for residue SO4 J 402

Chain	Residue
D	GLN91
J	LYS349
J	ARG352
J	ARG356

site_id	AF6
Number of Residues	4
Details	binding site for residue SO4 J 403

Chain	Residue
D	ARG352
J	LYS88
J	PRO347
J	ALA348

site_id	AF7
Number of Residues	9
Details	binding site for residue SPD J 404

Chain	Residue
J	TRP34
J	THR35
J	SER82
J	GLU181
J	TYR239
J	ASP242
J	TRP271
J	ASP273
J	TYR309

site_id	AF8
Number of Residues	2
Details	binding site for residue SO4 K 401

Chain	Residue
K	ARG356
K	ARG360

site_id	AF9
Number of Residues	5
Details	binding site for residue SO4 K 403

Chain	Residue
A	LYS349
A	ARG352
K	LYS88
K	PRO347
K	ALA348

site_id	AG1
Number of Residues	8
Details	binding site for residue SPD K 404

Chain	Residue
K	THR35
K	TYR37
K	SER82
K	GLU181
K	TYR239
K	ASP242
K	TRP271
K	ASP273

site_id	AG2
Number of Residues	4
Details	binding site for residue SO4 L 401

Chain	Residue
L	LYS88
L	PRO347
L	ALA348
R	ARG352

site_id	AG3
Number of Residues	4
Details	binding site for residue SO4 L 403

Chain	Residue
L	LYS349
L	ARG352
L	ARG356
R	GLN91

site_id	AG4
Number of Residues	10
Details	binding site for residue SPD L 404

Chain	Residue
L	TRP34
L	THR35
L	TYR37
L	SER82
L	GLU181
L	TYR239
L	ASP242
L	TRP271
L	ASP273
L	TYR309

site_id	AG5
Number of Residues	3
Details	binding site for residue SO4 M 401

Chain	Residue
M	LEU353
M	ARG356
M	ARG360

site_id	AG6
Number of Residues	4
Details	binding site for residue SO4 M 402

Chain	Residue
F	GLN91
M	LYS349
M	ARG352
M	ARG356

site_id	AG7
Number of Residues	4
Details	binding site for residue SO4 M 403

Chain	Residue
F	ARG352
M	LYS88
M	PRO347
M	ALA348

site_id	AG8
Number of Residues	4
Details	binding site for residue SO4 N 401

Chain	Residue
P	LYS203
P	LEU353
P	ARG356
P	ARG360

site_id	AG9
Number of Residues	3
Details	binding site for residue SO4 N 402

Chain	Residue
P	LYS349
P	ARG352
P	ARG356

site_id	AH1
Number of Residues	4
Details	binding site for residue SO4 N 403

Chain	Residue
N	LYS88
N	PRO347
N	ALA348
P	ARG352

site_id	AH2
Number of Residues	3
Details	binding site for residue SO4 N 404

Chain	Residue
N	LEU353
N	ARG356
N	ARG360

site_id	AH3
Number of Residues	4
Details	binding site for residue SO4 N 405

Chain	Residue
N	ARG352
P	LYS88
P	PRO347
P	ALA348

site_id	AH4
Number of Residues	4
Details	binding site for residue SO4 N 406

Chain	Residue
N	LYS349
N	ARG352
N	ARG356
P	GLN91

site_id	AH5
Number of Residues	1
Details	binding site for residue SO4 O 402

Chain	Residue
O	GLN91

site_id	AH6
Number of Residues	2
Details	binding site for residue SO4 O 403

Chain	Residue
O	PRO347
O	ALA348

site_id	AH7
Number of Residues	4
Details	binding site for residue SO4 O 404

Chain	Residue
O	LYS203
O	LEU353
O	ARG356
O	ARG360

site_id	AH8
Number of Residues	2
Details	binding site for residue SO4 O 405

Chain	Residue
O	LYS349
O	ARG352

site_id	AH9
Number of Residues	3
Details	binding site for residue SO4 O 406

Chain	Residue
O	LYS349
O	ARG352
O	ARG356

site_id	AI1
Number of Residues	12
Details	binding site for residue SPD Q 401

Chain	Residue
Q	TRP34
Q	THR35
Q	TYR37
Q	ASN62
Q	SER82
Q	GLU181
Q	SER221
Q	TYR239
Q	ASP242
Q	TRP271
Q	ASP273
Q	TYR309

site_id	AI2
Number of Residues	4
Details	binding site for residue SO4 R 401

Chain	Residue
R	LEU353
R	ARG356
R	THR357
R	ARG360

site_id	AI3
Number of Residues	4
Details	binding site for residue SO4 R 402

Chain	Residue
L	GLN91
R	LYS349
R	ARG352
R	ARG356

site_id	AI4
Number of Residues	4
Details	binding site for residue SO4 R 403

Chain	Residue
L	ARG352
R	LYS88
R	PRO347
R	ALA348

site_id	AI5
Number of Residues	17
Details	binding site for Di-peptide SPD B 405 and GLU B 181

Chain	Residue
B	TRP34
B	THR35
B	ASN62
B	SER82
B	ASN135
B	SER178
B	GLY179
B	ASP180
B	MET182
B	LEU183
B	ALA185
B	PHE237
B	TYR239
B	ASP242
B	TRP271
B	ASP273
B	TYR309

site_id	AI6
Number of Residues	16
Details	binding site for Di-peptide SPD C 404 and GLU C 181

Chain	Residue
C	TRP34
C	THR35
C	TYR37
C	SER82
C	ASN135
C	SER178
C	GLY179
C	ASP180
C	MET182
C	LEU183
C	ALA185
C	TYR239
C	ASP242
C	TRP271
C	ASP273
C	TYR309

site_id	AI7
Number of Residues	13
Details	binding site for Di-peptide SO4 E 403 and ARG E 352

Chain	Residue
E	ALA348
E	LYS349
E	VAL350
E	LEU351
E	LEU353
E	GLN354
E	THR355
E	ARG356
E	SO4404
H	LYS88
H	GLN91
H	PRO347
H	ALA348

site_id	AI8
Number of Residues	16
Details	binding site for Di-peptide SPD E 405 and GLU E 181

Chain	Residue
E	TRP34
E	THR35
E	TYR37
E	SER82
E	ASN135
E	MET176
E	SER178
E	GLY179
E	ASP180
E	MET182
E	PHE237
E	TYR239
E	ASP242
E	TRP271
E	ASP273
E	TYR309

site_id	AI9
Number of Residues	10
Details	binding site for Di-peptide SO4 H 402 and ARG H 352

Chain	Residue
E	GLN91
E	SO4401
H	ALA348
H	LYS349
H	VAL350
H	LEU351
H	LEU353
H	GLN354
H	THR355
H	ARG356

site_id	AJ1
Number of Residues	14
Details	binding site for Di-peptide SPD I 404 and GLU I 181

Chain	Residue
I	TRP34
I	THR35
I	SER82
I	ASN135
I	SER178
I	GLY179
I	ASP180
I	MET182
I	ALA185
I	TYR239
I	ASP242
I	TRP271
I	ASP273
I	TYR309

site_id	AJ2
Number of Residues	8
Details	binding site for Di-peptide SO4 K 402 and LYS K 349

Chain	Residue
A	GLN91
K	PRO347
K	ALA348
K	VAL350
K	LEU351
K	ARG352
K	LEU353
K	ARG356

site_id	AJ3
Number of Residues	11
Details	binding site for Di-peptide SO4 K 402 and ARG K 352

Chain	Residue
A	GLN91
A	ALA92
A	SO4401
K	ALA348
K	LYS349
K	VAL350
K	LEU351
K	LEU353
K	GLN354
K	THR355
K	ARG356

site_id	AJ4
Number of Residues	8
Details	binding site for Di-peptide SO4 L 402 and ARG L 356

Chain	Residue
L	ARG352
L	LEU353
L	THR355
L	THR357
L	TRP358
L	ARG360
L	SO4403
R	GLN91

site_id	AJ5
Number of Residues	15
Details	binding site for Di-peptide SPD M 404 and GLU M 181

Chain	Residue
M	TRP34
M	THR35
M	TYR37
M	SER82
M	SER178
M	GLY179
M	ASP180
M	MET182
M	ALA185
M	PHE237
M	TYR239
M	ASP242
M	TRP271
M	ASP273
M	TYR309

site_id	AJ6
Number of Residues	17
Details	binding site for Di-peptide SPD N 407 and GLU N 181

Chain	Residue
N	TRP34
N	THR35
N	TYR37
N	SER82
N	ASN135
N	SER178
N	ASP180
N	MET182
N	ALA185
N	SER221
N	PHE237
N	TYR239
N	ASP242
N	ASN269
N	TRP271
N	ASP273
N	TYR309

site_id	AJ7
Number of Residues	16
Details	binding site for Di-peptide SPD O 407 and GLU O 181

Chain	Residue
O	TRP34
O	THR35
O	TYR37
O	SER82
O	ASN135
O	SER178
O	GLY179
O	ASP180
O	MET182
O	ALA185
O	PHE237
O	TYR239
O	ASP242
O	TRP271
O	ASP273
O	TYR309

site_id	AJ8
Number of Residues	17
Details	binding site for Di-peptide SPD P 401 and GLU P 181

Chain	Residue
P	TRP34
P	THR35
P	TYR37
P	ASN62
P	SER82
P	ASN135
P	SER178
P	GLY179
P	ASP180
P	MET182
P	ALA185
P	PHE237
P	TYR239
P	ASP242
P	TRP271
P	ASP273
P	TYR309

site_id	AJ9
Number of Residues	16
Details	binding site for Di-peptide SPD R 404 and GLU R 181

Chain	Residue
R	TRP34
R	THR35
R	TYR37
R	SER82
R	ASN135
R	SER178
R	GLY179
R	ASP180
R	MET182
R	ALA185
R	PHE237
R	TYR239
R	ASP242
R	TRP271
R	ASP273
R	TYR309

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	72
Details	BINDING: BINDING => ECO:0000269\|PubMed:22300763

Chain	Residue	Details
A	THR35
C	GLU181
C	ASP242
C	ASN269
D	THR35
D	GLU181
D	ASP242
D	ASN269
E	THR35
E	GLU181
E	ASP242
A	GLU181
E	ASN269
F	THR35
F	GLU181
F	ASP242
F	ASN269
G	THR35
G	GLU181
G	ASP242
G	ASN269
H	THR35
A	ASP242
H	GLU181
H	ASP242
H	ASN269
I	THR35
I	GLU181
I	ASP242
I	ASN269
J	THR35
J	GLU181
J	ASP242
A	ASN269
J	ASN269
K	THR35
K	GLU181
K	ASP242
K	ASN269
L	THR35
L	GLU181
L	ASP242
L	ASN269
M	THR35
B	THR35
M	GLU181
M	ASP242
M	ASN269
N	THR35
N	GLU181
N	ASP242
N	ASN269
O	THR35
O	GLU181
O	ASP242
B	GLU181
O	ASN269
P	THR35
P	GLU181
P	ASP242
P	ASN269
Q	THR35
Q	GLU181
Q	ASP242
Q	ASN269
R	THR35
B	ASP242
R	GLU181
R	ASP242
R	ASN269
B	ASN269
C	THR35

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