7SMF: P107 pocket domain

p107 pocket domain complexed with mutated HDAC1-3X peptide. Determined by X-ray diffraction at 3.0 Å resolution. Released 29 Jun 2022.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,789
Mol. weight: 89.48 kDa
Released: 29 Jun 2022

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

Secondary structure: helices and β-sheets

7SMF contains 46 α-helices and 6 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: 22 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	392-400	9
α-helix	412-417	6
α-helix	424-442	19
β-strand	446	1	1
β-strand	449	1	1
α-helix	454-478	25
α-helix	480-483	4
α-helix	491-493	3
α-helix	495-512	18
α-helix	521-525	5
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-541	5
α-helix	549-564	16
α-helix	574-579	6
α-helix	788-809	22
α-helix	817-830	14
α-helix	840-853	14
α-helix	861-868	8
α-helix	877-880	4
β-strand	883	1	2
β-strand	927	1	2
α-helix	930-933	4
α-helix	934-938	5
α-helix	939-946	8
α-helix	962-964	3

Chain C: 24 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	454-478	25
α-helix	480-483	4
α-helix	490-493	4
α-helix	495-512	18
α-helix	521-525	5
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-542	6
α-helix	549-564	16
α-helix	573-579	7
α-helix	588-592	5
α-helix	787-809	23
α-helix	817-829	13
α-helix	832-835	4
α-helix	840-853	14
α-helix	861-869	9
α-helix	876-878	3
β-strand	883	1	3
β-strand	927	1	3
α-helix	930-933	4
α-helix	934-938	5
α-helix	939-946	8
α-helix	961-963	3

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>7SMF_1 Retinoblastoma-like protein 1 (chains A, C)
GEFTQSVSRLQSIVAGLKNAPSDQLINIFESCVRNPVENIMKILKGIGETFCQHYTQSTD
EQPGSHIDFAVNRLKLAEILYYKILETVMVQETRRLHGMDMSVLLEQDIFHRSLMACCLE
IVLFAYSSPRTFPWIIEVLNLQPFYFYKVIEVVIRSEEGLSRDMVKHLNSIEEQILESLA
WSHDSALWEALQVSANKVPTCEEVIFPNNFETGNNRPKRTGSLALFYRKVYHLASVRLRD
LCLKLDVSNELRRKIWTCFEFTLVHCPDLMKDRHLDQLLLCAFYIMAKVTKEERTFQEIM
KSYRNQPQANSHVYRSVLLKSIKEERGDLIKFYNTIYVGRVKSFALKYDLANQDHMMDAP
PLSPFPHIKQQ

Sequence of entity 2 (B, D), FASTA

>7SMF_2 Histone deacetylase 1 (chains B, D)
DIYCYEEFSD

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
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

Browse structure collections

About this viewer

MolViewer shows 7SMF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.