5LNC: PDB entry 5LNC

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1. Determined by X-ray diffraction at 3.29 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 3.29 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 2
Atoms: 4,673
Mol. weight: 84.47 kDa
Released: 9 Nov 2016

Explore 5LNC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LNC contains 28 α-helices and 16 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: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	13-15	3
α-helix	22-35	14
α-helix	42-87	46
β-strand	89	1	1
β-strand	91	1	1
α-helix	95-137	43
α-helix	143-151	9
α-helix	160-178	19
β-strand	188-191	4	2
β-strand	197-201	5	2
α-helix	205-207	3
β-strand	212-217	6	2
α-helix	225-250	26
α-helix	253-254	2
β-strand	258-262	5	2
β-strand	270-275	6	2
α-helix	276-278	3
α-helix	284-301	18
β-strand	306-309	4	2
α-helix	321-338	18
β-strand	346-350	5	2
α-helix	354-365	12

Chain B: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	13-15	3
α-helix	22-35	14
α-helix	42-88	47
α-helix	96-137	42
α-helix	143-151	9
α-helix	160-177	18
β-strand	186-191	6	3
β-strand	197-201	5	3
α-helix	205-207	3
β-strand	212-217	6	3
α-helix	225-250	26
α-helix	253-254	2
β-strand	258-262	5	3
β-strand	270-275	6	3
α-helix	276-278	3
α-helix	284-301	18
β-strand	306-309	4	3
α-helix	321-338	18
β-strand	346-350	5	3
α-helix	354-365	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar transporter chaperone 4,Core histone macro-H2A.1	A, B	protein	374	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens	O75367 (AlphaFold model), P47075 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5LNC_1 Vacuolar transporter chaperone 4,Core histone macro-H2A.1 (chains A, B)
MKFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFLESLEIELDKVY
TFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLAKFS
RLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGAG
SDGFTVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNTDFYIGGEVGNTLEKKGGKEFV
EAVLELRKKNGPLEVAGAAVSAGHGLPAKFVIHCNSPVWGADKCEELLEKTVKNCLALAD
DKKLKSIAFPSIGSGRNGFPKQTAAQLILKAISSYFVSTMSSSIKTVYFVLFDSESIGIY
VQEMAKLEHHHHHH

Primary citation

The macro domain as fusion tag for carrier-driven crystallization. Wild, R., Hothorn, M. Protein Sci (2017) 26:365-374. DOI 10.1002/pro.3073 · PubMed

Other PDB entries of the same protein (UniProt O75367 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HSV 1.43 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
1ZR3 1.66 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form B)
3IVB 1.75 Å, Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3…
3IID 1.9 Å, Crystal structure of the macro domain of human histone macroH2A1.1 in complex with…
3IIF 2.1 Å, Crystal structure of the macro domain of human histone macroH2A1.1 in complex with…
5IIT 2.13 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…
3HQH 2.3 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
2FXK 2.54 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form A)
2F8N 2.9 Å, 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes
9PM0 2.9 Å, nucleosome containing histone variant macroH2A
1ZR5 2.92 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.2
1U35 3.0 Å, Crystal structure of the nucleosome core particle containing the histone domain of…

Browse structure collections

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