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6m8p

Human ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013

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

Endoplasmic reticulum aminopeptidase 1

Homo sapiens

UniProt Q9NZ08

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 13 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
10 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 13 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
11 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 16 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
12 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
13 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 15 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
14 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
15 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
16 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 13 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
17 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 13 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
18 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 15 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
19 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
2 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
20 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
21 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 15 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
22 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 13 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
3 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
4 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
5 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
6 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
7 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 15 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
8 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count
9 Other combination Monomer Protein 1 其他Polymer 2 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide × 1 SULFATE ION × 14 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3qnf 3qnf 3rjo 5j5e 6t6r 9gjn 9gjn 9gjs 9gk6 9gke 9td3 9td4

15 assemblies; showing the first 12

Homodimer
7mwb 7mwb 7mwc 7mwc

4 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2yd0 3mdj 3mdj 3mdj 3qnf 6m8p 6m8p 6m8p 6m8p 6m8p 6m8p 6m8p

34 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ERAP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–899； UniProt 33–940 Author chain B； PDBConstruct 1–899； UniProt 33–940 Author chain C； PDBConstruct 1–899； UniProt 33–940 Author chain D； PDBConstruct 1–899； UniProt 33–940 Author chain E； PDBConstruct 1–899； UniProt 33–940 Author chain F； PDBConstruct 1–899； UniProt 33–940 Author chain G； PDBConstruct 1–899； UniProt 33–940 Author chain H； PDBConstruct 1–899； UniProt 33–940 Author chain I； PDBConstruct 1–899； UniProt 33–940 Author chain J； PDBConstruct 1–899； UniProt 33–940 Author chain K； PDBConstruct 1–899； UniProt 33–940 Author chain L； PDBConstruct 1–899； UniProt 33–940 Author chain M； PDBConstruct 1–899； UniProt 33–940 Author chain N； PDBConstruct 1–899； UniProt 33–940 Author chain O； PDBConstruct 1–899； UniProt 33–940 Author chain P； PDBConstruct 1–899； UniProt 33–940 Author chain Q； PDBConstruct 1–899； UniProt 33–940 Author chain R； PDBConstruct 1–899； UniProt 33–940 Author chain S； PDBConstruct 1–899； UniProt 33–940 Author chain T； PDBConstruct 1–899； UniProt 33–940 Author chain U； PDBConstruct 1–899； UniProt 33–940 Author chain V； PDBConstruct 1–899； UniProt 33–940

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_id6m8p
Deposition date deposition_date2018-08-22
Structure title titleHuman ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013
Keywords keywordsInhibitor, Aminopeptidase, Antigen processing, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
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.

6m8p__assembly_16__model_1

Assembly 16 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6m8p__assembly_16__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6m8p__assembly_16__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）29.26 Å
Rg (electron density)28.30 Å
Total Rg29.16 Å
Atom count7062
Residues861
Excluded volume126100 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6m8p__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6m8p__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6m8p__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6m8p__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 6m8p__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 6m8p__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 6m8p__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 6m8p__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 6m8p__assembly_9__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 6m8p__assembly_10__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
11 1 6m8p__assembly_11__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
12 1 6m8p__assembly_12__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
13 1 6m8p__assembly_13__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
14 1 6m8p__assembly_14__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
15 1 6m8p__assembly_15__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
16 1 6m8p__assembly_16__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
17 1 6m8p__assembly_17__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
18 1 6m8p__assembly_18__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
19 1 6m8p__assembly_19__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
20 1 6m8p__assembly_20__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
21 1 6m8p__assembly_21__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
22 1 6m8p__assembly_22__model_1 monomeric （1） 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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7. Citations (1)