7SME: P107 pocket domain

p107 pocket domain complexed with HDAC1 peptide. Determined by X-ray diffraction at 2.64 Å resolution. Released 29 Jun 2022.

Method: X-ray diffraction
Resolution: 2.64 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,883
Mol. weight: 44.66 kDa
Released: 29 Jun 2022

Explore 7SME in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SME contains 23 α-helices and 2 β-strands across 1 chain. 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: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	392-400	9
α-helix	410-418	9
α-helix	424-443	20
α-helix	454-477	24
α-helix	480-484	5
α-helix	489-492	4
α-helix	495-512	18
α-helix	521-525	5
α-helix	530-542	13
α-helix	549-564	16
α-helix	574-579	6
α-helix	585-587	3
α-helix	588-592	5
α-helix	787-809	23
α-helix	816-830	15
α-helix	832-835	4
α-helix	840-854	15
α-helix	861-868	8
α-helix	877-880	4
β-strand	883-885	3	1
β-strand	926-927	2	1
α-helix	930-933	4
α-helix	934-939	6
α-helix	940-947	8
α-helix	961-964	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoblastoma-like protein 1	A	protein	371	Homo sapiens	P28749 (AlphaFold model)
Histone deacetylase 1	B	protein	10	Homo sapiens	Q13547 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7SME_1 Retinoblastoma-like protein 1 (chains A)
GEFTQSVSRLQSIVAGLKNAPSDQLINIFESCVRNPVENIMKILKGIGETFCQHYTQSTD
EQPGSHIDFAVNRLKLAEILYYKILETVMVQETRRLHGMDMSVLLEQDIFHRSLMACCLE
IVLFAYSSPRTFPWIIEVLNLQPFYFYKVIEVVIRSEEGLSRDMVKHLNSIEEQILESLA
WSHDSALWEALQVSANKVPTCEEVIFPNNFETGNNRPKRTGSLALFYRKVYHLASVRLRD
LCLKLDVSNELRRKIWTCFEFTLVHCPDLMKDRHLDQLLLCAFYIMAKVTKEERTFQEIM
KSYRNQPQANSHVYRSVLLKSIKEERGDLIKFYNTIYVGRVKSFALKYDLANQDHMMDAP
PLSPFPHIKQQ

Sequence of entity 2 (B), FASTA

>7SME_2 Histone deacetylase 1 (chains B)
RIACEEEFSD

Primary citation

Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family. Putta, S., Alvarez, L., Ludtke, S. et al. Structure (2022) 30:1340. DOI 10.1016/j.str.2022.05.019 · 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
4YOO 2.4 Å, p107 pocket domain in complex with LIN52 P29A peptide
9C6B 2.6 Å, PP2A:B55-p107 substrate complex
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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