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6vim

P. putida mandelate racemase co-crystallized with phenylboronic acid

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

Mandelate racemase

Pseudomonas putida

UniProt P11444

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 8 MAGNESIUM ION × 8 PHENYL BORONIC ACID × 8 1,2-ETHANEDIOL × 15 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
1dtn 1mdl 1mdr 1mns 1mra 2mnr 3uxk 3uxk 3uxl 3uxl 4fp1 4hnc

17 assemblies; showing the first 12

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name MANR_PSEPU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 25–383； UniProt 1–359 Author chain B； PDBConstruct 25–383； UniProt 1–359 Author chain C； PDBConstruct 25–383； UniProt 1–359 Author chain D； PDBConstruct 25–383； UniProt 1–359 Author chain E； PDBConstruct 25–383； UniProt 1–359 Author chain F； PDBConstruct 25–383； UniProt 1–359 Author chain G； PDBConstruct 25–383； UniProt 1–359 Author chain H； PDBConstruct 25–383； UniProt 1–359

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_id6vim
Deposition date deposition_date2020-01-13
Structure title titleP. putida mandelate racemase co-crystallized with phenylboronic acid
Keywords keywordsInhibitor, Boronate, ISOMERASE, ISOMERASE-INHIBITOR complex; ISOMERASE/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.

6vim__assembly_1__model_1

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

Download this curve (.dat)

6vim__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6vim__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）40.51 Å
Rg (electron density)40.00 Å
Total Rg40.46 Å
Atom count21679
Residues2856
Excluded volume390380 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6vim__assembly_1__model_1 octameric （8） 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) 16 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd6vima1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamilyd.54.1 — Enolase N-terminal domain-like
Family Family familyd.54.1.0 — automated matches
Domain ID domain_idd6vima2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.11 — Enolase C-terminal domain-like
Family Family familyc.1.11.2 — D-glucarate dehydratase-like
Domain ID domain_idd6vimb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamilyd.54.1 — Enolase N-terminal domain-like
Family Family familyd.54.1.0 — automated matches
Domain ID domain_idd6vimb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.11 — Enolase C-terminal domain-like
Family Family familyc.1.11.2 — D-glucarate dehydratase-like
Domain ID domain_idd6vimc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamilyd.54.1 — Enolase N-terminal domain-like
Family Family familyd.54.1.0 — automated matches
Domain ID domain_idd6vimc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.11 — Enolase C-terminal domain-like
Family Family familyc.1.11.2 — D-glucarate dehydratase-like
Domain ID domain_idd6vimd1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamilyd.54.1 — Enolase N-terminal domain-like
Family Family familyd.54.1.0 — automated matches
Domain ID domain_idd6vimd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.11 — Enolase C-terminal domain-like
Family Family familyc.1.11.2 — D-glucarate dehydratase-like
Domain ID domain_idd6vime1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamilyd.54.1 — Enolase N-terminal domain-like
Family Family familyd.54.1.0 — automated matches
Domain ID domain_idd6vime2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.11 — Enolase C-terminal domain-like
Family Family familyc.1.11.2 — D-glucarate dehydratase-like
Domain ID domain_idd6vimf1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamilyd.54.1 — Enolase N-terminal domain-like
Family Family familyd.54.1.0 — automated matches
Domain ID domain_idd6vimf2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.11 — Enolase C-terminal domain-like
Family Family familyc.1.11.2 — D-glucarate dehydratase-like
Domain ID domain_idd6vimg1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamilyd.54.1 — Enolase N-terminal domain-like
Family Family familyd.54.1.0 — automated matches
Domain ID domain_idd6vimg2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.11 — Enolase C-terminal domain-like
Family Family familyc.1.11.2 — D-glucarate dehydratase-like
Domain ID domain_idd6vimh1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamilyd.54.1 — Enolase N-terminal domain-like
Family Family familyd.54.1.0 — automated matches
Domain ID domain_idd6vimh2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.11 — Enolase C-terminal domain-like
Family Family familyc.1.11.2 — D-glucarate dehydratase-like
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7. Citations (1)