6KYH: Shank3 NTD-ANK A42K mutant

Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas. Determined by X-ray diffraction at 3.3 Å resolution. Released 4 Dec 2019.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Mus musculus
Chains: 8
Atoms: 16,429
Mol. weight: 240.41 kDa
Ligands: MG, GNP
Released: 4 Dec 2019

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

Secondary structure: helices and β-sheets

6KYH contains 115 α-helices and 68 β-strands across 8 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: 23 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	1
α-helix	16-18	3
β-strand	20-26	7	1
β-strand	31	1	2
α-helix	32-42	11
α-helix	46-47	2
β-strand	54-57	4	1
β-strand	66-67	2	1
α-helix	68-69	2
β-strand	73	1	2
α-helix	74-76	3
α-helix	78-80	3
β-strand	87-91	5	1
α-helix	104-110	7
α-helix	113-125	13
α-helix	128-136	9
α-helix	152-156	5
α-helix	163-171	9
β-strand	179	1	3
β-strand	185	1	3
α-helix	186-192	7
α-helix	196-204	9
α-helix	219-226	8
α-helix	231-238	8
α-helix	241-243	3
α-helix	253-260	8
α-helix	263-271	9
α-helix	286-293	8
α-helix	296-304	9
α-helix	319-326	8
α-helix	329-337	9
α-helix	340-342	3

Chain B: 23 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	4
α-helix	16-18	3
β-strand	20-26	7	4
β-strand	31	1	5
α-helix	32-42	11
α-helix	46-47	2
β-strand	54-57	4	4
β-strand	66-67	2	4
α-helix	68-69	2
β-strand	73	1	5
α-helix	74-76	3
α-helix	78-80	3
β-strand	87-91	5	4
α-helix	101-103	3
α-helix	104-110	7
α-helix	113-124	12
α-helix	128-136	9
α-helix	152-157	6
α-helix	163-171	9
β-strand	179	1	6
β-strand	185	1	6
α-helix	186-192	7
α-helix	196-204	9
α-helix	219-226	8
α-helix	231-238	8
α-helix	253-260	8
α-helix	263-271	9
α-helix	286-293	8
α-helix	296-304	9
α-helix	319-326	8
α-helix	329-337	9
α-helix	340-342	3

Chain C: 21 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	7
β-strand	20-26	7	7
β-strand	31	1	8
α-helix	32-43	12
α-helix	50-52	3
β-strand	53-57	5	7
β-strand	66-67	2	7
α-helix	68-69	2
β-strand	73	1	8
α-helix	74-76	3
α-helix	78-80	3
β-strand	87-92	6	7
α-helix	105-110	6
α-helix	113-124	12
α-helix	128-136	9
α-helix	152-158	7
α-helix	163-171	9
β-strand	179	1	9
β-strand	185	1	9
α-helix	186-192	7
α-helix	196-204	9
α-helix	219-226	8
α-helix	231-238	8
α-helix	253-260	8
α-helix	263-271	9
α-helix	286-293	8
α-helix	296-304	9
α-helix	319-326	8
α-helix	329-337	9
α-helix	340-342	3

Chain D: 23 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	10
β-strand	20-26	7	10
β-strand	31	1	11
α-helix	32-43	12
α-helix	50-52	3
β-strand	53-57	5	10
α-helix	58-59	2
β-strand	66-67	2	10
α-helix	68-69	2
β-strand	73	1	11
α-helix	74-76	3
α-helix	78-80	3
β-strand	87-92	6	10
α-helix	104-110	7
α-helix	113-124	12
α-helix	128-136	9
α-helix	152-158	7
α-helix	163-171	9
β-strand	179	1	12
β-strand	185	1	12
α-helix	186-192	7
α-helix	196-204	9
α-helix	219-226	8
α-helix	231-238	8
α-helix	253-260	8
α-helix	263-271	9
α-helix	286-293	8
α-helix	296-304	9
α-helix	319-326	8
α-helix	329-337	9
α-helix	340-342	3
α-helix	349-351	3

Chain E: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	62-67	6
α-helix	68-74	7
β-strand	77-83	7	1
α-helix	87-104	18
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
β-strand	145	1	16
β-strand	150	1	16
α-helix	152-165	14

Chain F: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	4
α-helix	16-25	10
β-strand	37-46	10	4
β-strand	49-58	10	4
α-helix	62-67	6
α-helix	68-74	7
β-strand	77-83	7	4
α-helix	87-104	18
β-strand	111-116	6	4
α-helix	127-137	11
β-strand	141-143	3	4
β-strand	145	1	13
β-strand	150	1	13
α-helix	152-166	15

Chain G: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	7
α-helix	16-25	10
β-strand	37-46	10	7
β-strand	49-58	10	7
α-helix	59	1
α-helix	62-67	6
α-helix	68-74	7
β-strand	77-83	7	7
α-helix	87-104	18
β-strand	111-116	6	7
α-helix	127-137	11
β-strand	141-143	3	7
β-strand	145	1	14
β-strand	150	1	14
α-helix	152-165	14

Chain H: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	10
α-helix	16-25	10
β-strand	37-46	10	10
β-strand	49-58	10	10
α-helix	63-65	3
α-helix	68-74	7
β-strand	77-83	7	10
α-helix	87-104	18
β-strand	111-116	6	10
α-helix	127-137	11
β-strand	141-143	3	10
β-strand	145	1	15
β-strand	150	1	15
α-helix	152-165	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SH3 and multiple ankyrin repeat domains protein 3	A, B, C, D	protein	361	Mus musculus	Q4ACU6 (AlphaFold model)
GTPase HRas	E, F, G, H	protein	171	Mus musculus	Q61411 (AlphaFold model)

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

>6KYH_1 SH3 and multiple ankyrin repeat domains protein 3 (chains A, B, C, D)
GPGSEFAVVVRVGIPDLQQTKCLRLDPTAPVWAAKQRVLCKLNHSLQDALNYGLFQPPSR
GRAGKFLDEERLLQDYPPNLDTPLPYLEFRYKRRVYAQNLIDDKQFAKLHTKANLKKFMD
YVQLHSTDKVARLLDKGLDPNFHDPDSGECPLSLAAQLDNATDLLKVLRNGGAHLDFRTR
DGLTAVHCATRQRNAGALTTLLDLGASPDYKDSRGLTPLYHSALGGGDARCCELLLHDHA
QLGTTDENGWQEIHQACRFGHVQHLEHLLFYGANMGAQNASGNTALHICALYNQESCARV
LLYRGANKDVRNYNSQTAFQVAIIAGNFELAEVIKTHKDSDVVPFRETPSYAKRRRLAGP
S

Sequence of entity 2 (E, F, G, H), FASTA

>6KYH_2 GTPase HRas (chains E, F, G, H)
GPGSMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDIL
DTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGN
KCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	4

Primary citation

Shank3 Binds to and Stabilizes the Active Form of Rap1 and HRas GTPases via Its NTD-ANK Tandem with Distinct Mechanisms. Cai, Q., Hosokawa, T., Zeng, M. et al. Structure (2020) 28:290. DOI 10.1016/j.str.2019.11.018 · PubMed

Other PDB entries of the same protein (UniProt Q4ACU6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3O5N 1.83 Å, Tetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a…
32CR 1.98 Å, SHANK3 PDZ (570-664) in complex with an internal PDZ binding motif (843-864) in Densin-180
5IZU 2.49 Å, A new binding site outside the canonical PDZ domain determines the specific interaction…
9KSQ 2.79 Å, Crystal Structure of the mouse Shank3 SAM domain
6KYK 2.82 Å, Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1

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