6IKM | pdb_00006ikm

Crystal structure of SpuE-Spermidine in complex with ScFv5

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
Y [auth M]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
W [auth L]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
U [auth K]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
S [auth J]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
Q [auth I]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
O [auth H]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
M [auth G]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
K [auth F]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
IA [auth R]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
GA [auth Q]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
EA [auth P]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
CA [auth O]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
AA [auth N]	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8076239	3000083	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
Z [auth m]	Ribonuc_L-PSP	e6ikmm1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
X [auth l]	Ribonuc_L-PSP	e6ikml1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
V [auth k]	Ribonuc_L-PSP	e6ikmk1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
T [auth j]	Ribonuc_L-PSP	e6ikmj1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
R [auth i]	Ribonuc_L-PSP	e6ikmi1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
P [auth h]	Ribonuc_L-PSP	e6ikmh1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
N [auth g]	Ribonuc_L-PSP	e6ikmg1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
L [auth f]	Ribonuc_L-PSP	e6ikmf1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
JA [auth r]	Ribonuc_L-PSP	e6ikmr1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
J [auth e]	Ribonuc_L-PSP	e6ikme1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
HA [auth q]	Ribonuc_L-PSP	e6ikmq1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
H [auth d]	Ribonuc_L-PSP	e6ikmd1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
FA [auth p]	Ribonuc_L-PSP	e6ikmp1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
F [auth c]	Ribonuc_L-PSP	e6ikmc1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
DA [auth o]	Ribonuc_L-PSP	e6ikmo1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
D [auth b]	Ribonuc_L-PSP	e6ikmb1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
BA [auth n]	Ribonuc_L-PSP	e6ikmn1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
B [auth a]	Ribonuc_L-PSP	e6ikma1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
Y [auth M]	Ribonuc_L-PSP	e6ikmM1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
W [auth L]	Ribonuc_L-PSP	e6ikmL1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
U [auth K]	Ribonuc_L-PSP	e6ikmK1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
S [auth J]	Ribonuc_L-PSP	e6ikmJ1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
Q [auth I]	Ribonuc_L-PSP	e6ikmI1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
O [auth H]	Ribonuc_L-PSP	e6ikmH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
M [auth G]	Ribonuc_L-PSP	e6ikmG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
K [auth F]	Ribonuc_L-PSP	e6ikmF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
IA [auth R]	Ribonuc_L-PSP	e6ikmR1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
I [auth E]	Ribonuc_L-PSP	e6ikmE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
GA [auth Q]	Ribonuc_L-PSP	e6ikmQ1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
G [auth D]	Ribonuc_L-PSP	e6ikmD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
EA [auth P]	Ribonuc_L-PSP	e6ikmP1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
E [auth C]	Ribonuc_L-PSP	e6ikmC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
CA [auth O]	Ribonuc_L-PSP	e6ikmO1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
C [auth B]	Ribonuc_L-PSP	e6ikmB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
AA [auth N]	Ribonuc_L-PSP	e6ikmN1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)
A	Ribonuc_L-PSP	e6ikmA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: Ribonuc_L-PSP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
Z [auth m]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
X [auth l]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
V [auth k]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
T [auth j]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
R [auth i]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
P [auth h]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
N [auth g]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
L [auth f]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
JA [auth r]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
J [auth e]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
HA [auth q]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
H [auth d]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
FA [auth p]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F [auth c]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
DA [auth o]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth b]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
BA [auth n]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth a]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
Y [auth M]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
W [auth L]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
U [auth K]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
S [auth J]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
Q [auth I]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
O [auth H]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
M [auth G]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
K [auth F]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
IA [auth R]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
I [auth E]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
GA [auth Q]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
G [auth D]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
EA [auth P]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
E [auth C]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
CA [auth O]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
C [auth B]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
AA [auth N]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth a], BA [auth n], D [auth b], DA [auth o], F [auth c], B [auth a], BA [auth n], D [auth b], DA [auth o], F [auth c], FA [auth p], H [auth d], HA [auth q], J [auth e], JA [auth r], L [auth f], N [auth g], P [auth h], R [auth i], T [auth j], V [auth k], X [auth l], Z [auth m]	scFv 5, anti-SpuE	SCFV-HEAVY-LAMBDA	Homo sapiens (human)	IGHV1-202, IGHJ604, IGLV1-5101, IGLJ201, IGLJ3*01	V-DOMAIN VH, V-DOMAIN V-LAMBDA	IG	SCFV-HEAVY-LAMBDA	IMGT (202615-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, AA [auth N], C [auth B], CA [auth O], E [auth C], A, AA [auth N], C [auth B], CA [auth O], E [auth C], EA [auth P], G [auth D], GA [auth Q], I [auth E], IA [auth R], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	PF13416	Bacterial extracellular solute-binding protein (SBP_bac_8)	Bacterial extracellular solute-binding protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth a], BA [auth n], D [auth b], DA [auth o], F [auth c], B [auth a], BA [auth n], D [auth b], DA [auth o], F [auth c], FA [auth p], H [auth d], HA [auth q], J [auth e], JA [auth r], L [auth f], N [auth g], P [auth h], R [auth i], T [auth j], V [auth k], X [auth l], Z [auth m]	ScFv5	-	-	-
A, AA [auth N], C [auth B], CA [auth O], E [auth C], A, AA [auth N], C [auth B], CA [auth O], E [auth C], EA [auth P], G [auth D], GA [auth Q], I [auth E], IA [auth R], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	Polyamine transport protein	cation binding polyamine binding binding ion binding amine binding putrescine binding small molecule binding spermidine binding	localization nitrogen compound transport putrescine transport transport establishment of localization polyamine transport organic cation transport	cellular anatomical structure extracellular region outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, AA [auth N], C [auth B], CA [auth O], E [auth C], A, AA [auth N], C [auth B], CA [auth O], E [auth C], EA [auth P], G [auth D], GA [auth Q], I [auth E], IA [auth R], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A, AA [auth N], C [auth B], CA [auth O], E [auth C], A, AA [auth N], C [auth B], CA [auth O], E [auth C], EA [auth P], G [auth D], GA [auth Q], I [auth E], IA [auth R], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	IPR001188	Spermidine/putrescine-binding periplasmic protein	Family

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.