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5i58

GLUTAMATE- AND GLYCINE-BOUND GLUN1/GLUN2A AGONIST BINDING DOMAINS WITH MPX-004

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1

Rattus norvegicus

UniProt P35439

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A × 1 （Q00959） GLYCINE × 1 GLUTAMIC ACID × 1 5-({[(3-chloro-4-fluorophenyl)sulfonyl]amino}methyl)-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1pb7 1pb8 1pb9 1pbq 1pbq 1y1m 1y1m 1y1z 1y20 4kfq 4kfq 6ove

12 assemblies

Homodimer
1y1m 3q41 3q41 4kcc

4 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2a5t 4nf4 4nf5 4nf6 4nf8 4pe5 5dex 5fxg 5fxh 5fxi 5fxj 5fxk

105 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NMDZ1_RAT
Isoform P35439-6
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–152； UniProt 415–565 Author chain A； PDBConstruct 155–292； UniProt 684–821

Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A

Rattus norvegicus

UniProt Q00959

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1 × 1 （P35439） GLYCINE × 1 GLUTAMIC ACID × 1 5-({[(3-chloro-4-fluorophenyl)sulfonyl]amino}methyl)-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2a5s 6ove

2 assemblies

Homodimer
2a5s

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2a5t 4nf4 4nf5 4nf6 4nf8 5dex 5i56 5i57 5i58 5i59 5jty 5tpw

59 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NMDE1_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–139； UniProt 402–539 Author chain B； PDBConstruct 142–281； UniProt 661–800

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_id5i58
Deposition date deposition_date2016-02-14
Structure title titleGLUTAMATE- AND GLYCINE-BOUND GLUN1/GLUN2A AGONIST BINDING DOMAINS WITH MPX-004
Keywords keywordsNMDA receptor, Antagonist, TRANSPORT PROTEIN, RECEPTOR; TRANSPORT PROTEIN, RECEPTOR
Experimental Method methodX-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.

5i58__assembly_1__model_1

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

Download this curve (.dat)

5i58__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5i58__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）25.61 Å
Rg (electron density)24.38 Å
Total Rg25.33 Å
Atom count4290
Residues534
Excluded volume76658 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5i58__assembly_1__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 (6)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5i58a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like
Domain ID domain_idd5i58b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id5i58A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id5i58A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id5i58B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id5i58B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
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7. Citations (1)