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BMRB: 18559

2LV9

Solution NMR structure of the PHD domain of human MLL5. Northeast structural genomics consortium target HR6512A.

Authors

Lemak, A., Yee, A., Houliston, S., Garcia, M., Wu, H., Min, J., Arrowsmith, C.

Assembly

MLL5

Entity

1. MLL5 (polymer, Thiol state: free and other bound), 98 monomers, 11497.69 Da Detail

MHHHHHHSSG RENLYFQGSE DGSYGTDVTR CICGFTHDDG YMICCDKCSV WQHIDCMGID RQHIPDTYLC ERCQPRNLDK ERAVLLQRRK RENMSDGD

2. ZINC ION (non-polymer, Thiol state: not present), 65.409 × 2 Da

Total weight

11628.509 Da

Max. entity weight

11497.69 Da

Entity Connection

na 7 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS31:SG	2:ZN1:ZN
2	na	sing	1:CYS33:SG	2:ZN1:ZN
3	na	sing	1:CYS56:SG	2:ZN1:ZN
4	na	sing	1:CYS45:SG	2:ZN1:ZN
5	na	sing	1:CYS48:SG	2:ZN1:ZN
6	na	sing	1:CYS70:SG	2:ZN1:ZN
7	na	sing	1:CYS73:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

restrained molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 77.6 %, Completeness: 71.7 %, Completeness (bb): 73.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.7 % (797 of 1112)	71.0 % (414 of 583)	72.4 % (307 of 424)	72.4 % (76 of 105)
Backbone	73.5 % (429 of 584)	72.8 % (147 of 202)	74.5 % (213 of 286)	71.9 % (69 of 96)
Sidechain	70.7 % (437 of 618)	70.1 % (267 of 381)	71.5 % (163 of 228)	77.8 % (7 of 9)
Aromatic	46.0 % (46 of 100)	46.0 % (23 of 50)	44.9 % (22 of 49)	100.0 % (1 of 1)
Methyl	93.5 % (58 of 62)	93.5 % (29 of 31)	93.5 % (29 of 31)

1. MLL5

MHHHHHHSSG RENLYFQGSE DGSYGTDVTR CICGFTHDDG YMICCDKCSV WQHIDCMGID RQHIPDTYLC ERCQPRNLDK ERAVLLQRRK RENMSDGD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	MLL5	[U-13C; U-15N]	0.5 mM
2	TRIS	natural abundance	10 mM
3	sodium chloride	natural abundance	300 mM
4	ZnSO4	natural abundance	10 uM
5	DTT	natural abundance	1 mM
6	NaN3	natural abundance	0.01 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LV9, Strand ID: A Detail

Release date

2012-07-30

Citation

Solution NMR structure and histone binding of the PHD domain of human MLL5
Lemak, A., Yee, A., Wu, H., Yap, D., Zeng, H., Dombrovski, L., Houliston, S., Aparicio, S., Arrowsmith, C.H.
PLoS One (2013), 8, e77020-e77020, PubMed 24130829 , DOI 10.1371/journal.pone.0077020 , Abstract

Related entities 1. MLL5, : 1 : 2 : 14 entities Detail

Interaction partners 1. MLL5, : 8 interactors Detail

More details for 8 interactors identified by 3 citations

Experiments performed 9 experiments Detail

1 3D HNCO