7SMD: P107 pocket domain

p107 pocket domain complexed with EID1 peptide. Determined by X-ray diffraction at 2.15 Å resolution. Released 29 Jun 2022.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,950
Mol. weight: 45.09 kDa
Released: 29 Jun 2022

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

Secondary structure: helices and β-sheets

7SMD contains 25 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: 25 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	392-401	10
α-helix	410-418	9
α-helix	424-442	19
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	574-580	7
α-helix	585-587	3
α-helix	588-592	5
α-helix	787-809	23
α-helix	814-830	17
α-helix	832-835	4
α-helix	840-855	16
α-helix	861-868	8
α-helix	877-880	4
β-strand	882-885	4	1
β-strand	926-928	3	1
α-helix	930-933	4
α-helix	934-938	5
α-helix	939-946	8
α-helix	947-949	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoblastoma-like protein 1	A	protein	371	Homo sapiens	P28749 (AlphaFold model)
EP300-interacting inhibitor of differentiation 1	B	protein	14	Homo sapiens	Q9Y6B2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7SMD_1 Retinoblastoma-like protein 1 (chains A)
GEFTQSVSRLQSIVAGLKNAPSDQLINIFESCVRNPVENIMKILKGIGETFCQHYTQSTD
EQPGSHIDFAVNRLKLAEILYYKILETVMVQETRRLHGMDMSVLLEQDIFHRSLMACCLE
IVLFAYSSPRTFPWIIEVLNLQPFYFYKVIEVVIRSEEGLSRDMVKHLNSIEEQILESLA
WSHDSALWEALQVSANKVPTCEEVIFPNNFETGNNRPKRTGSLALFYRKVYHLASVRLRD
LCLKLDVSNELRRKIWTCFEFTLVHCPDLMKDRHLDQLLLCAFYIMAKVTKEERTFQEIM
KSYRNQPQANSHVYRSVLLKSIKEERGDLIKFYNTIYVGRVKSFALKYDLANQDHMMDAP
PLSPFPHIKQQ

Sequence of entity 2 (B), FASTA

>7SMD_2 EP300-interacting inhibitor of differentiation 1 (chains B)
LTEELGCDEIIDRE

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:

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
7SMF 3.0 Å, p107 pocket domain complexed with mutated HDAC1-3X peptide

Browse structure collections

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