4YOO: P107 pocket domain

p107 pocket domain in complex with LIN52 P29A peptide. Determined by X-ray diffraction at 2.4 Å resolution. Released 13 May 2015.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,082
Mol. weight: 45.78 kDa
Released: 13 May 2015

Explore 4YOO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YOO contains 26 α-helices and 2 β-strands across 2 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: 25 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	392-401	10
α-helix	410-417	8
α-helix	424-443	20
α-helix	454-478	25
α-helix	480-483	4
α-helix	489-492	4
α-helix	495-512	18
α-helix	521-525	5
α-helix	530-533	4
α-helix	535-543	9
α-helix	549-564	16
α-helix	566-568	3
α-helix	573-580	8
α-helix	589-591	3
α-helix	787-806	20
α-helix	819-830	12
α-helix	832-835	4
α-helix	840-854	15
α-helix	862-864	3
α-helix	865-868	4
α-helix	876-880	5
β-strand	882-883	2	1
β-strand	927-928	2	1
α-helix	930-933	4
α-helix	934-938	5
α-helix	939-946	8
α-helix	961-964	4

Chain X: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoblastoma-like protein 1,Retinoblastoma-like protein 1	A	protein	369	Homo sapiens	P28749 (AlphaFold model)
LIN52 peptide	X	protein	20	Homo sapiens	Q52LA3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4YOO_1 Retinoblastoma-like protein 1,Retinoblastoma-like protein 1 (chains A)
GEFTQSVSRLQSIVAGLKNAPSDQLINIFESCVRNPVENIMKILKGIGETFCQHYTQSTD
EQPGSHIDFAVNRLKLAEILYYKILETVMVQETRRLHGMDMSVLLEQDIFHRSLMACCLE
IVLFAYSSPRTFPWIIEVLNLQPFYFYKVIEVVIRSEEGLSRDMVKHLNSIEEQILESLA
WSHDSALWEALQVSANKVPTCEEVIFPNNFETGRPKRTGSLALFYRKVYHLASVRLRDLC
LKLDVSNELRRKIWTCFEFTLVHCPDLMKDRHLDQLLLCAFYIMAKVTKEERTFQEIMKS
YRNQPQANSHVYRSVLLKSIKEERGDLIKFYNTIYVGRVKSFALKYDLANQDHMMDAPPL
SPFPHIKQQ

Sequence of entity 2 (X), FASTA

>4YOO_2 LIN52 peptide (chains X)
EASLLSFEKLDRASADLWPE

Primary citation

Structural mechanisms of DREAM complex assembly and regulation. Guiley, K.Z., Liban, T.J., Felthousen, J.G. et al. Genes Dev (2015) 29:961-974. DOI 10.1101/gad.257568.114 · PubMed

Other PDB entries of the same protein (UniProt P28749 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SMD 2.15 Å, p107 pocket domain complexed with EID1 peptide
4YOZ 2.25 Å, p107 pocket domain in complex with HPV E7 peptide
4YOS 2.3 Å, p107 pocket domain complexed with LIN52 peptide
9C6B 2.6 Å, PP2A:B55-p107 substrate complex
7SME 2.64 Å, p107 pocket domain complexed with HDAC1 peptide
7SMC 2.7 Å, p107 pocket domain complexed with ARID4A peptide
1H28 2.8 Å, CDK2/CyclinA in complex with an 11-residue recruitment peptide from p107
5TUV 2.9 Å, Crystal structure of the E2F5-DP1-p107 ternary complex
7SMF 3.0 Å, p107 pocket domain complexed with mutated HDAC1-3X peptide

Browse structure collections

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