3MNN | pdb_00003mnn

A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core

PDB DOI: https://doi.org/10.2210/pdb3MNN/pdb
NAKB: 3MNN

Classification: STRUCTURAL PROTEIN/DNA
Organism(s): Xenopus laevis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-04-22 Released: 2011-04-06
Deposition Author(s): Ong, M.S., Davey, C.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.277 (Depositor), 0.269 (DCC)
R-Value Work:
0.247 (Depositor), 0.240 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A ruthenium antimetastasis agent forms specific histone protein adducts in the nucleosome core

Wu, B., Ong, M.S., Groessl, M., Adhireksan, Z., Hartinger, C.G., Dyson, P.J., Davey, C.A.

(2011) Chemistry 17: 3562-3566

PubMed: 21344528 Search on PubMed
DOI: https://doi.org/10.1002/chem.201100298
Primary Citation Related Structures:
3MNN

Organizational Affiliation

Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.

Macromolecule Content

Total Structure Weight: 197.69 kDa
Atom Count: 12,126
Modeled Residue Count: 1,055
Deposited Residue Count: 1,252
Unique protein chains: 4
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	135	Xenopus laevis	Mutation(s): 0 Gene Names: HISTONE H3
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84233
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Xenopus laevis	Mutation(s): 0 Gene Names: HISTONE H4
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	119	Xenopus laevis	Mutation(s): 0 Gene Names: HISTONE H2A, LOC494591
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06897
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	125	Xenopus laevis	Mutation(s): 0 Gene Names: HISTONE H2B
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02281
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
DNA (145-MER)	I	145	N/A
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
DNA (145-MER)	J	145	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTW Query on PTW Download:Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain S [auth G] SDF format, chain O [auth F] MOL2 format, chain W [auth H] MOL2 format, chain S [auth G] MOL2 format, chain O [auth F] mmCIF format, chain W [auth H] mmCIF format, chain S [auth G] mmCIF format, chain O [auth F]	O [auth F], S [auth G], W [auth H]	1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane C₆ H₁₂ N₃ P FXXRPTKTLVHPAR-UHFFFAOYSA-N		Interactions Focus chain O [auth F] Focus chain S [auth G] Focus chain W [auth H] Interactions & Density Focus chain O [auth F] Focus chain S [auth G] Focus chain W [auth H]
MML Query on MML Download:Ideal Coordinates CCD File SDF format, chain V [auth H] SDF format, chain R [auth G] SDF format, chain N [auth F] MOL2 format, chain V [auth H] MOL2 format, chain R [auth G] MOL2 format, chain N [auth F] mmCIF format, chain V [auth H] mmCIF format, chain R [auth G] mmCIF format, chain N [auth F]	N [auth F], R [auth G], V [auth H]	1-methyl-4-(1-methylethyl)benzene C₁₀ H₁₄ HFPZCAJZSCWRBC-UHFFFAOYSA-N		Interactions Focus chain N [auth F] Focus chain R [auth G] Focus chain V [auth H] Interactions & Density Focus chain N [auth F] Focus chain R [auth G] Focus chain V [auth H]
RU Query on RU Download:Ideal Coordinates CCD File SDF format, chain U [auth H] SDF format, chain Q [auth G] SDF format, chain M [auth F] MOL2 format, chain U [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain M [auth F] mmCIF format, chain U [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain M [auth F]	M [auth F], Q [auth G], U [auth H]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N		Interactions Focus chain M [auth F] Focus chain Q [auth G] Focus chain U [auth H] Interactions & Density Focus chain M [auth F] Focus chain Q [auth G] Focus chain U [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth H] SDF format, chain P [auth G] SDF format, chain K [auth D] MOL2 format, chain T [auth H] MOL2 format, chain P [auth G] MOL2 format, chain K [auth D] mmCIF format, chain T [auth H] mmCIF format, chain P [auth G] mmCIF format, chain K [auth D]	K [auth D], P [auth G], T [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth D] Focus chain P [auth G] Focus chain T [auth H] Interactions & Density Focus chain K [auth D] Focus chain P [auth G] Focus chain T [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth E] MOL2 format, chain L [auth E] mmCIF format, chain L [auth E]	L [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth E] Interactions & Density Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.277 (Depositor), 0.269 (DCC)
R-Value Work: 0.247 (Depositor), 0.240 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.35	α = 90
b = 109.86	β = 90
c = 182.59	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Ong, M.S.

Davey, C.A.

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description