7KNX: SND1

Crystal structure of SND1 in complex with C-26-A6. Determined by X-ray diffraction at 2.7 Å resolution. Released 8 Dec 2021.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,995
Mol. weight: 148.87 kDa
Ligands: QOV, TYR
Released: 8 Dec 2021

Explore 7KNX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KNX contains 63 α-helices and 72 β-strands across 4 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.

Chains A, B and D: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	20-27	8	1
α-helix	29-31	3
β-strand	33-36	4	1
α-helix	44-45	2
β-strand	46-51	6	1
β-strand	54-55	2	2
α-helix	57-60	4
β-strand	61-62	2	3
β-strand	72-73	2	3
α-helix	74-76	3
α-helix	79-90	12
β-strand	94-102	9	1
β-strand	108-114	7	1
β-strand	121-122	2	1
α-helix	123-129	7
β-strand	134-135	2	2
α-helix	144-157	14
α-helix	162-164	3
α-helix	170-172	3
β-strand	177	1	4
α-helix	183-189	7
β-strand	195-204	10	4
β-strand	207-212	6	4
β-strand	217-223	7	4
β-strand	226-227	2	5
α-helix	241-242	2
α-helix	245-256	12
β-strand	260-269	10	4
β-strand	272-278	7	4
α-helix	284-290	7
β-strand	295-296	2	5
α-helix	300-303	4
α-helix	308-320	13
α-helix	324-326	3

Chain C: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	20-27	8	11
α-helix	29-31	3
β-strand	33-36	4	11
α-helix	43-45	3
β-strand	46-51	6	11
β-strand	54-55	2	12
α-helix	57-60	4
β-strand	61-62	2	8
β-strand	72-73	2	8
α-helix	74-76	3
α-helix	79-90	12
β-strand	94-102	9	11
β-strand	108-114	7	11
β-strand	121-122	2	11
α-helix	123-129	7
β-strand	134-135	2	12
α-helix	144-157	14
α-helix	162-164	3
α-helix	170-172	3
β-strand	177	1	13
α-helix	183-189	7
β-strand	195-204	10	13
β-strand	207-212	6	13
β-strand	217-223	7	13
β-strand	226-227	2	14
α-helix	245-256	12
β-strand	260-269	10	13
β-strand	272-278	7	13
α-helix	284-290	7
β-strand	295-296	2	14
α-helix	300-303	4
α-helix	308-320	13
α-helix	324-326	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Staphylococcal nuclease domain-containing protein 1	A, B, C, D	protein	324	Homo sapiens	Q7KZF4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7KNX_1 Staphylococcal nuclease domain-containing protein 1 (chains A, B, C, D)
MGSSHHHHHHSSGENLYFQGVPTVQRGIIKMVLSGCAIIVRGQPRGGPPPERQINLSNIR
AGNLARRAAKDTPDEPWAFPAREFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGE
NIAESLVAEGLATRREGMRANNPEQNRLSECEEQAKAAKKGMWSEGNGSHTIRDLKYTIE
NPRHFVDSHHQKPVNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFRRETPEPFAA
EAKFFTESRLLQRDVQIILESCHNQNILGTILHPNGNITELLLKEGFARCVDWSIAVYTR
GAEKLRAAERFAKERRLRIWRDYV

Ligands and cofactors

ID	Name	Formula	Copies
QOV	5-chloro-2-methoxy-N-(2-methyl[1,2,4]triazolo[1,5-a]pyridin-8-yl)benzene-1-sulf…	C14 H13 Cl N4 O3 S	4
TYR	Tyrosine	C9 H11 N O3	1

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

Primary citation

Small-molecule inhibitors that disrupt the MTDH-SND1 complex suppress breast cancer progression and metastasis. Shen, M., Wei, Y., Kim, H. et al. Nat Cancer (2022) 3:43-59. DOI 10.1038/s43018-021-00279-5 · PubMed

Other PDB entries of the same protein (UniProt Q7KZF4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HQX 1.42 Å, Crystal structure of human P100 tudor domain conserved region
5M9O 1.45 Å, Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically…
3OMC 1.77 Å, Structure of human SND1 extended tudor domain in complex with the symmetrically…
3OMG 1.85 Å, Structure of human SND1 extended tudor domain in complex with the symmetrically…
3BDL 1.9 Å, Crystal structure of a truncated human Tudor-SN
2HQE 2.0 Å, Crystal structure of human P100 Tudor domain: Large fragment
2O4X 2.0 Å, Crystal structure of human P100 tudor domain
7KNW 2.65 Å, Crystal structure of SND1 in complex with C-26-A2
4QMG 2.7 Å, The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting Interactions
2E6N Solution structure of the TUDOR domain of Staphylococcal nuclease domain-containing…

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