8VTS

Meis1 homeobox domain bound to paromomycin fragment

PDB DOI: https://doi.org/10.2210/pdb8VTS/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-27 Released: 2024-02-14
Deposition Author(s): Tomchick, D.R., Ahmed, M.S., Nguyen, N.U.N.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Cancer Prevention and Research Institute of Texas (CPRIT), Leducq Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association, Robert A. Welch Foundation, Leukemia & Lymphoma Society, European Research Council (ERC), British Heart Foundation, European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.211
R-Value Work: 0.191
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Identification of FDA-Approved Drugs That Induce Heart Regeneration in Mammals

Ahmed, M.S., Nguyen, N.U.N., Nakada, Y., Hsu, C.-C., Farag, A., Lam, N.T., Wang, P., Thet, S., Menendez-Montes, I., Elhelaly, W.M., Lou, X., Secco, I., Tomczyk, M., Zentilin, L., Pei, J., Cui, M., Dos Santos, M., Liu, X., Liu, Y., Zaha, D., Walcott, G., Tomchick, D.R., Xing, C., Zhang, C.-C., Grishin, N.V., Giacca, M., Zhang, J., Sadek, H.A.

To be published.

Macromolecule Content

Total Structure Weight: 63.66 kDa
Atom Count: 4,282
Modelled Residue Count: 447
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Meis1	A, B, C, D, E A, B, C, D, E, F, G, H	67	Mus musculus	Mutation(s): 0 Gene Names: Meis1
UniProt & NIH Common Fund Data Resources
Find proteins for Q60954 (Mus musculus) Explore Q60954 Go to UniProtKB: Q60954
IMPC: MGI:104717
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60954
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIO (Subject of Investigation/LOI) Query on RIO Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth D] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D]	J [auth B], L [auth D]	RIBOSTAMYCIN C₁₇ H₃₄ N₄ O₁₀ NSKGQURZWSPSBC-VVPCINPTSA-N		Interactions Focus chain J [auth B] Focus chain L [auth D] Interactions & Density Focus chain J [auth B] Focus chain L [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth F] MOL2 format, chain O [auth F]	O [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth F] Interactions & Density Focus chain O [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth D] SDF format, chain Q [auth H] MOL2 format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth H]	I [auth B], M [auth D], Q [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain M [auth D] Focus chain Q [auth H] Interactions & Density Focus chain I [auth B] Focus chain M [auth D] Focus chain Q [auth H]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain N [auth E] SDF format, chain P [auth G] MOL2 format, chain K [auth C] MOL2 format, chain N [auth E] MOL2 format, chain P [auth G]	K [auth C], N [auth E], P [auth G]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain N [auth E] Focus chain P [auth G] Interactions & Density Focus chain K [auth C] Focus chain N [auth E] Focus chain P [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.211
R-Value Work: 0.191
R-Value Observed: 0.192
Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.621	α = 90
b = 77.621	β = 90
c = 213.724	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-14

Deposition Author(s):

Tomchick, D.R.

Ahmed, M.S.

Nguyen, N.U.N.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL137415-02
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL147276-01
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL149137-01
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP160520
Leducq Foundation	France	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119336
American Heart Association	United States	856552
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM127390
Robert A. Welch Foundation	United States	I-1505
Leukemia & Lymphoma Society	United States	6629-21
European Research Council (ERC)	European Union	787971
British Heart Foundation	United Kingdom	RG/19/11/34633
European Commission	European Union	825670
European Commission	European Union	874764