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Crystal structure of a putative lipoprotein (BDI_3050) from Parabacteroides distasonis ATCC 8503 at 2.70 A resolution

X-ray diffraction
2.7Å resolution
PDB entry 4fvs coloured by chain, front view.
PDB entry 4fvs coloured by chain, side view.
PDB entry 4fvs coloured by chain, top view.
Source organism: Parabacteroides distasonis ATCC 8503
Assembly composition:
monomeric (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1
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Assembly Name: DUF3108 domain-containing protein
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Multimeric state: monomeric
Accessible surface area: 10705.28 Å2
Buried surface area: 0.0 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-107950
Monomeric assembly 1 of PDB entry 4fvs coloured by chemically distinct molecules, front view.
Monomeric assembly 1 of PDB entry 4fvs coloured by chemically distinct molecules, side view.
Monomeric assembly 1 of PDB entry 4fvs coloured by chemically distinct molecules, top view.
    Assembly 1
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA
Assembly 2
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Assembly Name: DUF3108 domain-containing protein
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Multimeric state: monomeric
Accessible surface area: 10758.03 Å2
Buried surface area: 0.0 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-107950
Monomeric assembly 2 of PDB entry 4fvs coloured by chemically distinct molecules, front view.
Monomeric assembly 2 of PDB entry 4fvs coloured by chemically distinct molecules, side view.
Monomeric assembly 2 of PDB entry 4fvs coloured by chemically distinct molecules, top view.
    Assembly 2
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA
Assembly 3
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Assembly Name: DUF3108 domain-containing protein
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Multimeric state: monomeric
Accessible surface area: 10638.32 Å2
Buried surface area: 272.16 Å2
Dissociation area: 65.98 Å2
Dissociation energy (ΔGdiss): 7.86 kcal/mol
Dissociation entropy (TΔSdiss): -0.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-107950
Monomeric assembly 3 of PDB entry 4fvs coloured by chemically distinct molecules, front view.
Monomeric assembly 3 of PDB entry 4fvs coloured by chemically distinct molecules, side view.
Monomeric assembly 3 of PDB entry 4fvs coloured by chemically distinct molecules, top view.
    Assembly 3
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA
Assembly 4 (preferred)
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Assembly Name: DUF3108 domain-containing protein
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Multimeric state: monomeric
Accessible surface area: 11007.82 Å2
Buried surface area: 143.27 Å2
Dissociation area: 71.64 Å2
Dissociation energy (ΔGdiss): 10.69 kcal/mol
Dissociation entropy (TΔSdiss): -0.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-107950
Monomeric assembly 4 of PDB entry 4fvs coloured by chemically distinct molecules, front view.
Monomeric assembly 4 of PDB entry 4fvs coloured by chemically distinct molecules, side view.
Monomeric assembly 4 of PDB entry 4fvs coloured by chemically distinct molecules, top view.
    Assembly 4
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA
Assembly 5
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Assembly Name: DUF3108 domain-containing protein
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Multimeric state: monomeric
Accessible surface area: 10663.75 Å2
Buried surface area: 0.0 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-107950
Monomeric assembly 5 of PDB entry 4fvs coloured by chemically distinct molecules, front view.
Monomeric assembly 5 of PDB entry 4fvs coloured by chemically distinct molecules, side view.
Monomeric assembly 5 of PDB entry 4fvs coloured by chemically distinct molecules, top view.
    Assembly 5
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA
Assembly 6
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Assembly Name: DUF3108 domain-containing protein
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Multimeric state: monomeric
Accessible surface area: 10712.93 Å2
Buried surface area: 95.18 Å2
Dissociation area: 47.59 Å2
Dissociation energy (ΔGdiss): 6.84 kcal/mol
Dissociation entropy (TΔSdiss): -0.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-107950
Monomeric assembly 6 of PDB entry 4fvs coloured by chemically distinct molecules, front view.
Monomeric assembly 6 of PDB entry 4fvs coloured by chemically distinct molecules, side view.
Monomeric assembly 6 of PDB entry 4fvs coloured by chemically distinct molecules, top view.
    Assembly 6
Confidence : 72%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : Unclear
Symmetry : Unclear
Evidence : This biological assembly agrees with the prediction of EPPIC but not of PISA

Macromolecules

DUF3108 domain-containing protein
Chains: A, B, C, D, E, F
Length: 215 amino acids
Theoretical weight: 24.7 KDa
Source organism: Parabacteroides distasonis ATCC 8503
Expression system: Escherichia coli
UniProt:
  • Canonical: A6LGE3 (Residues: 21-234; Coverage: 100%)
Gene name: BDI_3050
Pfam: DUF3108-like
CATH: YmcC-like fold
DUF3108 domain-containing protein in PDB entry 4fvs, assembly 4, front view.
DUF3108 domain-containing protein in PDB entry 4fvs, assembly 4, side view.
DUF3108 domain-containing protein in PDB entry 4fvs, assembly 4, top view.
PDBe-KB: UniProt Coverage View: A6LGE3  
121520406080100120140160180200
 
100200
UniProt
A6LGE3
Chains
Domains
Secondary structure
Flexibility predictions
Early folding residue predictions
Ligand binding sites
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