SAXSdb — 2rkm

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

OLIGO-PEPTIDE BINDING PROTEIN

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 26–542	Not recorded	LYS LYSINE × 2 IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；7% PEG 4K, 50MM SODIUM ACETATE PH5.5, 1MM URANYL ACETATE AND 30MG/ML OPPA	Resolution 1.80 Å R-free 0.219

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2RKM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B05 Structure of oligo-peptide binding protein complexed with LYS-CYS-LYS Deposited 1998-11-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	U1 URANIUM ATOM × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 2.00 Å R-free 0.243
1B1H OLIGO-PEPTIDE BINDING PROTEIN/TRIPEPTIDE (LYS HPE LYS) COMPLEX Deposited 1998-11-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.50	Resolution 1.80 Å R-free 0.220
1B2H Oligo-Peptide Binding Protein Complexed with Lysyl-Ornithyl-Lysine Deposited 1998-11-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	ACT ACETATE ION × 1 U1 URANIUM ATOM × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.90 Å R-free 0.220
1B32 OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KMK Deposited 1998-12-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8 ACT ACETATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.75 Å R-free 0.214
1B3F OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KHK Deposited 1998-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.80 Å R-free 0.217
1B3G OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KIK Deposited 1998-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 2.00 Å R-free 0.238
1B3H OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-CYCLOHEXYLALANYL-LYSINE Deposited 1998-11-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	U1 URANIUM ATOM × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.00 Å R-free 0.240
1B3L OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KGK Deposited 1998-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 2.00 Å R-free 0.241
1B3L OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KGK Deposited 1998-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 2.00 Å R-free 0.241
1B40 OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KFK Deposited 1998-11-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 2.20 Å R-free 0.258
1B46 OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KPK Deposited 1999-01-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8 ACT ACETATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.80 Å R-free 0.217
1B4Z OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KDK Deposited 1999-01-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8 ACT ACETATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.75 Å R-free 0.214
1B51 OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KSK Deposited 1999-01-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.80 Å R-free 0.223
1B52 OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KTK Deposited 1999-01-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 2.30 Å R-free 0.263
1B58 OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KYK Deposited 1999-01-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.80 Å R-free 0.223
1B5H OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-DIAMINOPROPANOIC ACID-LYSINE Deposited 1998-11-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	U1 URANIUM ATOM × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.90 Å R-free 0.230
1B5I OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KNK Deposited 1999-01-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	U1 URANIUM ATOM × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.90 Å R-free 0.223
1B5J OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KQK Deposited 1999-01-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	U1 URANIUM ATOM × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.80 Å R-free 0.227
1B6H OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORVALYL-LYSINE Deposited 1998-11-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–543（517 aa）	Not recorded	U1 URANIUM ATOM × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.80 Å R-free 0.220
1B7H OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-NORLEUCYL-LYSINE Deposited 1998-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–543（517 aa）	Not recorded	U1 URANIUM ATOM × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.00 Å R-free 0.260
1B9J OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KLK Deposited 1999-02-11	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.80 Å R-free 0.219
1JET OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KAK Deposited 1996-07-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.20 Å R-free 0.255
1JEU OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KEK Deposited 1996-07-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.25 Å R-free 0.252
1JEV OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KWK Deposited 1996-07-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.30 Å R-free 0.226
1OLA THE STRUCTURAL BASIS OF MULTISPECIFICITY IN THE OLIGOPEPTIDE-BINDING PROTEIN OPPA Deposited 1994-04-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1OLC OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH LYS-LYS-LYS-ALA Deposited 1995-09-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.10 Å R-free 0.197
1QKA OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KRK Deposited 1999-07-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.80 Å R-free 0.222
1QKB OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KVK Deposited 1999-07-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8 ACT ACETATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；CO-CRYSTALLIZED WITH URANIUM ACETATE, PH 5.5	Resolution 1.80 Å R-free 0.215
1RKM STRUCTURE OF OPPA Deposited 1997-03-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–542（517 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；3M (NH4)2SO4, 0.1M HEPES PH7.5, 0.2M NACL AND 20MG/ML OPPA	Resolution 2.40 Å R-free 0.247
2OLB OLIGOPEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH TRI-LYSINE Deposited 1995-09-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–542（517 aa）	Not recorded	IUM URANYL (VI) ION × 8 ACT ACETATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.40 Å

29 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OPPA_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–517； UniProt 26–542

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	2rkm
Deposition date deposition_date	1997-03-25
Structure title title	STRUCTURE OF OPPA COMPLEXED WITH LYS-LYS
Keywords keywords	PEPTIDE TRANSPORT, COMPLEX (BINDING PROTEIN-DIPEPTIDE), Peptide BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.76 Å
Radius of gyration Rg (electron density) rg_electron	23.46 Å
Forward intensity I(0) i0	65487500.00
Molecular weight molecular_weight	61222.0 kDa
Excluded volume excluded_volume	74970 Å³
Envelope volume envelope_volume	86854 Å³
Hydration-shell volume shell_volume	30221 Å³
Envelope diameter envelope_diameter	81.6 Å
Shell Rg shell_rg	31.26 Å
Envelope Rg envelope_rg	23.57 Å
Shape Rg shape_rg	23.26 Å
Total Rg total_rg	24.84 Å
Total atoms total_atoms	4207
Residues n_residues	517
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	84.2 Å
Rg (real space) rg_real	24.63 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	6.5490e+07
I(0) uncertainty (real space) i0_real_error	1.0050e+06
Rg (reciprocal space) rg_reciprocal	24.66 Å
I(0) (reciprocal space) i0_reciprocal	65490000.0000
Solution quality estimate total_estimate	0.7907
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	30.7 Å
Skewness Skewness skewness	0.225
Kurtosis Kurtosis kurtosis	-0.398
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9605000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	OLIGO-PEPTIDE BINDING PROTEIN
Molecular weight formula_weight	58879.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4750

ADVPAGVQLADKQTLVRNNGSEVQSLDPHKIEGVPESNVSRDLFEGLLISDVEGHPSPGVAEKWENKDFKVWTFHLRENAKWSDGTPVTAHDFVYSWQRLADPNTASPYASYLQYGHIANIDDIIAGKKPATDLGVKALDDHTFEVTLSEPVPYFYKLLVHPSVSPVPKSAVEKFGDKWTQPANIVTNGAYKLKNWVVNERIVLERNPQYWDNAKTVINQVTYLPISSEVTDVNRYRSGEIDMTYNNMPIELFQKLKKEIPNEVRVDPYLCTYYYEINNQKAPFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEWFKWSQQKRNEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWCADYNEPTSFLNTMLSDSSNNTAHYKSPAFDKLIADTLKVADDTQRSELYAKAEQQLDKDSAIVPVYYYVNARLVKPWVGGYTGKDPLDNIYVKNLYIIKH

Entity 2 Entity 2 non-polymer

Description description	LYSINE
Molecular weight formula_weight	147.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	URANYL (VI) ION
Molecular weight formula_weight	270.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2rkma_
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 (3 domains)

Domain ID domain_id	2rkmA01
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	2rkmA02
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	2rkmA03
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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8. Citations (5)

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Unit-cell length a length_a	110.470 Å
Unit-cell length b length_b	77.150 Å
Unit-cell length c length_c	71.590 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1670
R_free r_free	0.2190

fit	/app/data/saxs_computation/rk/2rkm/2rkm.fit
pddf	/app/data/pr_computation/rk/2rkm/2rkm.pr.out
profile	/app/data/saxs_computation/rk/2rkm/2rkm.dat

STRUCTURE OF OPPA COMPLEXED WITH LYS-LYS

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

OLIGO-PEPTIDE BINDING PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction