3tcf

Crystal structure of E. coli OppA complexed with endogenous ligands

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Periplasmic oligopeptide-binding protein

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Endogenous peptide × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Endogenous peptide × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Endogenous peptide × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Endogenous peptide × 1 water × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Endogenous peptide × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Endogenous peptide × 1 water × 1	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Endogenous peptide × 1 water × 1	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Endogenous peptide × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OPPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–518； UniProt 27–543 Author chain B； PDBConstruct 2–518； UniProt 27–543 Author chain C； PDBConstruct 2–518； UniProt 27–543 Author chain D； PDBConstruct 2–518； UniProt 27–543 Author chain E； PDBConstruct 2–518； UniProt 27–543 Author chain F； PDBConstruct 2–518； UniProt 27–543 Author chain G； PDBConstruct 2–518； UniProt 27–543 Author chain H； PDBConstruct 2–518； UniProt 27–543

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3tcf
Deposition date deposition_date	2011-08-09
Structure title title	Crystal structure of E. coli OppA complexed with endogenous ligands
Keywords keywords	Peptide-binding protein, PROTEIN TRANSPORT, peptide transport, ABC transporter; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3tcf__assembly_7__model_1

Assembly 7 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3tcf__assembly_7__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3tcf__assembly_7__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.04 Å
Rg (electron density)	23.18 Å
Total Rg	24.18 Å
Atom count	4138
Residues	520
Excluded volume	73490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3tcf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3tcf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3tcf__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3tcf__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3tcf__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3tcf__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3tcf__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3tcf__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Periplasmic oligopeptide-binding protein
Molecular weight formula_weight	59387.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	35615

MADVPAGVTLAEKQTLVRNNGSEVQSLDPHKIEGVPESNISRDLFEGLLVSDLDGHPAPGVAESWDNKDAKVWTFHLRKDAKWSDGTPVTAQDFVYSWQRSVDPNTASPYASYLQYGHIAGIDEILEGKKPITDLGVKAIDDHTLEVTLSEPVPYFYKLLVHPSTSPVPKAAIEKFGEKWTQPGNIVTNGAYTLKDWVVNERIVLERSPTYWNNAKTVINQVTYLPIASEVTDVNRYRSGEIDMTNNSMPIELFQKLKKEIPDEVHVDPYLCTYYYEINNQKPPFNDVRVRTALKLGMDRDIIVNKVKAQGNMPAYGYTPPYTDGAKLTQPEWFGWSQEKRNEEAKKLLAEAGYTADKPLTINLLYNTSDLHKKLAIAASSLWKKNIGVNVKLVNQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSNSSMNTAHYKSPAFDSIMAETLKVTDEAQRTALYTKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNTYTRNMYIVKHHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Endogenous peptide
Molecular weight formula_weight	273.3 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N,O,P

XXX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2408

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3tcfa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d3tcfb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d3tcfc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d3tcfd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d3tcfe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d3tcff_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d3tcfg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d3tcfh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

CATH v4.4 (24 domains)

Domain ID domain_id	3tcfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3tcfA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	3tcfA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

Domain ID domain_id	3tcfB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3tcfB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	3tcfB03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

Domain ID domain_id	3tcfC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3tcfC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	3tcfC03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

Domain ID domain_id	3tcfD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3tcfD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	3tcfD03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

Domain ID domain_id	3tcfE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3tcfE02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	3tcfE03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

Domain ID domain_id	3tcfF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3tcfF02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	3tcfF03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

Domain ID domain_id	3tcfG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3tcfG02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	3tcfG03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

Domain ID domain_id	3tcfH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	3tcfH02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	76 — Dipeptide-binding Protein; domain 1
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 1

Domain ID domain_id	3tcfH03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

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Unit-cell length a length_a	62.619 Å
Unit-cell length b length_b	202.599 Å
Unit-cell length c length_c	208.947 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	48.370 Å
R factor r_factor	0.2306
R_work r_work	0.2287
R_free r_free	0.2666

Crystal structure of E. coli OppA complexed with endogenous ligands

1. Protein Identity and Related Structures Protein Identity & Related Structures

Periplasmic oligopeptide-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3tcf__assembly_7__model_1

3tcf__assembly_7__model_1 | I(q)

3tcf__assembly_7__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of E. coli OppA complexed with endogenous ligands

1. Protein Identity and Related Structures Protein Identity & Related Structures

Periplasmic oligopeptide-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3tcf__assembly_7__model_1

3tcf__assembly_7__model_1 | I(q)

3tcf__assembly_7__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

CATH v4.4 (24 domains)

7. Citations (1)