1hr9

Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide

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

MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT

Saccharomyces cerevisiae

UniProt P11914

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT × 1 (P10507) MALATE DEHYDROGENASE × 1 (P17505) ZINC ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT × 1 (P10507) MALATE DEHYDROGENASE × 1 (P17505) ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT × 1 (P10507) MALATE DEHYDROGENASE × 1 (P17505) ZINC ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT × 1 (P10507) MALATE DEHYDROGENASE × 1 (P17505) ZINC ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name MPPA_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–469; UniProt 14–482 Author chain C; PDBConstruct 1–469; UniProt 14–482 Author chain E; PDBConstruct 1–469; UniProt 14–482 Author chain G; PDBConstruct 1–469; UniProt 14–482

MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT

Saccharomyces cerevisiae

UniProt P10507

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT × 1 (P11914) MALATE DEHYDROGENASE × 1 (P17505) ZINC ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT × 1 (P11914) MALATE DEHYDROGENASE × 1 (P17505) ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT × 1 (P11914) MALATE DEHYDROGENASE × 1 (P17505) ZINC ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT × 1 (P11914) MALATE DEHYDROGENASE × 1 (P17505) ZINC ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name MPPB_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–443; UniProt 21–462 Author chain D; PDBConstruct 2–443; UniProt 21–462 Author chain F; PDBConstruct 2–443; UniProt 21–462 Author chain H; PDBConstruct 2–443; UniProt 21–462

MALATE DEHYDROGENASE

OrganismNot specified

UniProt P17505

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT × 1 (P11914) MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT × 1 (P10507) ZINC ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT × 1 (P11914) MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT × 1 (P10507) ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT × 1 (P11914) MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT × 1 (P10507) ZINC ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT × 1 (P11914) MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT × 1 (P10507) ZINC ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name MDHM_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain O; PDBConstruct 1–8; UniProt 2–9 Author chain P; PDBConstruct 1–8; UniProt 2–9 Author chain Q; PDBConstruct 1–8; UniProt 2–9 Author chain R; PDBConstruct 1–8; UniProt 2–9

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_id1hr9
Deposition date deposition_date2000-12-21
Structure title titleYeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide
Keywords keywordsHxxEH zinc-binding motif, HYDROLASE; HYDROLASE
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.

1hr9__assembly_1__model_1

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

Download this curve (.dat)

1hr9__assembly_1__model_1 | I(q)

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

1hr9__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)30.25 Å
Rg (electron density)29.10 Å
Total Rg29.93 Å
Atom count6977
Residues899
Excluded volume124100 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1hr9__assembly_1__model_1 trimeric (3) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1hr9__assembly_2__model_1 trimeric (3) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1hr9__assembly_3__model_1 trimeric (3) Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1hr9__assembly_4__model_1 trimeric (3) 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 (5)

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6. Fold Classification (SCOP + CATH) 33 domains

SCOP 2.08 (17 domains)

Domain ID domain_idd1hr9a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9b1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9b2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9c1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9c2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9d1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9e1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9e2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9f1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9f2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9f3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1hr9g1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9g2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9h1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like
Domain ID domain_idd1hr9h2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.185 — LuxS/MPP-like metallohydrolase
Superfamily Superfamily superfamilyd.185.1 — LuxS/MPP-like metallohydrolase
Family Family familyd.185.1.1 — MPP-like

CATH v4.4 (16 domains)

Domain ID domain_id1hr9A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9C01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9C02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9D01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9D02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9E01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9E02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9F01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9F02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9G01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9G02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9H01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
Domain ID domain_id1hr9H02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Metalloenzyme, LuxS/M16 peptidase-like
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7. Citations (1)