6I8B: Spindlin1

Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn. Determined by X-ray diffraction at 1.76 Å resolution. Released 5 Dec 2018.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,293
Mol. weight: 53.11 kDa
Ligands: PO4, GLY, H7T
Released: 5 Dec 2018

Explore 6I8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6I8B contains 11 α-helices and 40 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 B: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	57-62	6	1
β-strand	70-79	10	1
β-strand	86-91	6	1
β-strand	96	1	2
β-strand	98-101	4	1
β-strand	108-114	7	1
α-helix	115-116	2
β-strand	119	1	3
α-helix	128-132	5
β-strand	136-142	7	2
β-strand	148-158	11	2
β-strand	166-170	5	2
β-strand	173-174	2	2
β-strand	175	1	4
β-strand	176-179	4	2
α-helix	181-186	6
β-strand	190-192	3	2
α-helix	193-194	2
β-strand	217-220	4	4
β-strand	228-235	8	4
β-strand	242-247	6	4
β-strand	252	1	1
β-strand	254-257	4	4
α-helix	261-263	3
β-strand	266-268	3	4

Chain E: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	57-62	6	5
β-strand	70-79	10	5
β-strand	86-91	6	5
β-strand	96	1	6
β-strand	97-101	5	5
β-strand	108-113	6	5
α-helix	116-118	3
α-helix	130-132	3
β-strand	136-142	7	6
β-strand	143	1	3
β-strand	148-158	11	6
β-strand	166-170	5	6
β-strand	173-174	2	6
β-strand	175	1	7
β-strand	176-179	4	6
α-helix	181-186	6
β-strand	190-192	3	6
α-helix	193	1
β-strand	217-221	5	7
β-strand	227-235	9	7
β-strand	242-247	6	7
β-strand	252	1	5
α-helix	253	1
β-strand	254-257	4	7
α-helix	261-263	3
β-strand	267-268	2	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spindlin-1	B, E	protein	222	Homo sapiens	Q9Y657 (AlphaFold model)

Sequence of entity 1 (B, E), FASTA

>6I8B_1 Spindlin-1 (chains B, E)
MPRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDER
VSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFY
ITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEYAKEDGSK
RTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTSAENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
GLY	Glycine	C2 H5 N O2	2
H7T	2-[4-[2-[[2-[3-[2-azanyl-5-(cyclopropylmethoxy)-3,3-dimethyl-indol-6-yl]oxyprop…	C42 H58 N8 O4	2

Water and common crystallization additives (DMS) are not listed.

Primary citation

A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function. Fagan, V., Johansson, C., Gileadi, C. et al. J Med Chem (2019) 62:9008-9025. DOI 10.1021/acs.jmedchem.9b00562 · PubMed

Other PDB entries of the same protein (UniProt Q9Y657 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OCB 1.42 Å, Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B
6I8Y 1.52 Å, Crystal structure of Spindlin1 in complex with the Methyltransferase inhibitor A366
6I8L 1.58 Å, Crystal structure of Spindlin1 in complex with the inhibitor TD001851a
6QPL 1.6 Å, Crystal structure of Spindlin1 in complex with the inhibitor MS31
7CNA 1.6 Å, Crystal structure of Spindlin1/C11orf84 complex bound to histone H3K4me3K9me3 peptide
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
8GTX 1.8 Å, Crystal Structure of human Spindlin1-HBx complex
9T2Z 1.87 Å, Spindlin 1 with crystallization epitope mutations H127D:L128D:T131R
4H75 2.1 Å, Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
2NS2 2.2 Å, Crystal Structure of Spindlin1
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

Browse structure collections

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