PDB 6x86 biological assemblies and structure analysis ‹ Protein Data Bank in Europe (PDBe)

Assemblies

Assembly 1 (preferred)

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Assembly Name: Transmembrane tumor necrosis factor complex
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Multimeric state: homo trimer

Accessible surface area: 18460.69 Å²

Buried surface area: 5644.4 Å²

Dissociation area: 1,822.91 Å²

Dissociation energy (ΔG^diss): 6.36 kcal/mol

Dissociation entropy (TΔS^diss): 12.51 kcal/mol

Symmetry number: 1

PDBe Complex ID: PDB-CPX-134285

$Homo trimeric assembly 1 of PDB entry 6x86 coloured by chemically distinct molecules, front view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>3 copies of Tumor necrosis factor;</li> <li class='image_legend_li'>1 copy of 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Homo trimeric assembly 1 of PDB entry 6x86 coloured by chemically distinct molecules, side view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>3 copies of Tumor necrosis factor;</li> <li class='image_legend_li'>1 copy of 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Homo trimeric assembly 1 of PDB entry 6x86 coloured by chemically distinct molecules, top view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>3 copies of Tumor necrosis factor;</li> <li class='image_legend_li'>1 copy of 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

Assembly 2

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Assembly Name: Transmembrane tumor necrosis factor complex
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Multimeric state: homo trimer

Accessible surface area: 17511.07 Å²

Buried surface area: 5990.87 Å²

Dissociation area: 1,653.77 Å²

Dissociation energy (ΔG^diss): 10.03 kcal/mol

Dissociation entropy (TΔS^diss): 12.5 kcal/mol

Symmetry number: 1

PDBe Complex ID: PDB-CPX-134285

$Homo trimeric assembly 2 of PDB entry 6x86 coloured by chemically distinct molecules, front view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>3 copies of Tumor necrosis factor;</li> <li class='image_legend_li'>1 copy of 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Homo trimeric assembly 2 of PDB entry 6x86 coloured by chemically distinct molecules, side view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>3 copies of Tumor necrosis factor;</li> <li class='image_legend_li'>1 copy of 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

$Homo trimeric assembly 2 of PDB entry 6x86 coloured by chemically distinct molecules, top view. This structure contains: <ul class='image_legend_ul'><li class='image_legend_li'>3 copies of Tumor necrosis factor;</li> <li class='image_legend_li'>1 copy of 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile;</li> <li class='image_legend_li'>1 copy of water.</li></ul>}$

Macromolecules

Tumor necrosis factor, soluble form

Chains: A, B, C, D, E, F
Length: 158 amino acids
Theoretical weight: 17.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:

Canonical: P01375 (Residues: 77-233; Coverage: 67%)

Gene names: TNF, TNFA, TNFSF2
Pfam: TNF(Tumour Necrosis Factor) family
InterPro:

Tumour necrosis factor-like domain superfamily
Tumour necrosis factor
Tumour necrosis factor domain
Tumour necrosis factor alpha
Tumour necrosis factor, conserved site

Tumor necrosis factor in PDB entry 6x86, assembly 1, front view.

Tumor necrosis factor in PDB entry 6x86, assembly 1, side view.

Tumor necrosis factor in PDB entry 6x86, assembly 1, top view.

FASTA Sequence


    >pdb|6x86|A B C D E F

MVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

PDBe-KB: UniProt Coverage View: P01375

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UniProt

P01375

Mapping to UniProt TNFA_HUMAN

Chains

RSRZ Outlier Chain A

Chain A

Chain B

RSRZ Outlier Chain C

Chain C

Chain D

RSRZ Outlier Chain E

Chain E

Chain F

Domains

Residues mapped to InterPro annotations

Secondary structure

Residues forming Helix

Residues forming Strand

Ligand binding sites

Residues binding 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile <img src="https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/UTY_200.svg" />

Interaction interfaces

Residues interacting with Tumor necrosis factor (P01375)

Sequence conservation

Amino acid probabilities The amino acid probabilities are calculated using HMM profiles based on multiple sequence alignments. Click to see more details...

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Molecule details ›

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FASTA (Protein chains A, B, C, D, E, F)
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Structure Factors
SIFTS XML file with residue-level mappings

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BLAST P01375 (UniProt)

Protein Data Bank in Europe

Crystal Structure of TNFalpha with indolinone compound 11

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Assemblies

Assembly 1 (preferred)

Assembly 2

Macromolecules

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PDBe › 6x86 › Structure analysis

Crystal Structure of TNFalpha with indolinone compound 11

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Assembly 1 (preferred)

Assembly 2

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6x86 › Structure analysis