3IK5: SIVmac239 Nef

SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80). Determined by X-ray diffraction at 2.05 Å resolution. Released 2 Feb 2010.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Simian immunodeficiency virus
Chains: 4
Atoms: 2,341
Mol. weight: 37.73 kDa
Released: 2 Feb 2010

Explore 3IK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3IK5 contains 19 α-helices and 16 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	102-108	7
β-strand	109	1	1
α-helix	113-126	14
α-helix	132	1
β-strand	133	1	2
α-helix	134	1
α-helix	136-148	13
β-strand	152	1	1
β-strand	159	1	3
β-strand	166	1	2
α-helix	167	1
β-strand	168	1	3
β-strand	175-179	5	2
β-strand	211-215	5	2
α-helix	217-220	4
α-helix	224-228	5
α-helix	230-232	3

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	64-72	9
α-helix	73-75	3

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	109	1	4
α-helix	113-126	14
α-helix	132	1
β-strand	133	1	5
α-helix	134	1
α-helix	136-148	13
β-strand	152	1	4
β-strand	159	1	6
β-strand	166	1	5
β-strand	168	1	6
β-strand	175-179	5	5
β-strand	211-215	5	5
α-helix	217-220	4
α-helix	224-228	5
α-helix	230-232	3

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	64-73	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein Nef	A, C	protein	143	Simian immunodeficiency virus	P31818
T-cell surface glycoprotein CD3 zeta chain	B, D	protein	18		P20963 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3IK5_1 Protein Nef (chains A, C)
GSDDLVGVSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGI
IPDWQDYTSGPGIRYPKTFGWLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVLA
WKFDPTLAYTYEAYVRYPEEFGS

Sequence of entity 2 (B, D), FASTA

>3IK5_2 T-cell surface glycoprotein CD3 zeta chain (chains B, D)
AYQQGQNQLYNELNLGRR

Primary citation

Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments. Kim, W.M., Sigalov, A.B., Stern, L.J. Acta Crystallogr D Biol Crystallogr (2010) 66:163-175. DOI 10.1107/S090744490904880X · PubMed

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