6KYK: Shank3 NTD-ANK mutant

Crystal structure of Shank3 NTD-ANK mutant in complex with Rap1. Determined by X-ray diffraction at 2.82 Å resolution. Released 4 Dec 2019.

Method: X-ray diffraction
Resolution: 2.82 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 11,209
Mol. weight: 162.23 kDa
Ligands: MG, GNP
Released: 4 Dec 2019

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

Secondary structure: helices and β-sheets

6KYK contains 73 α-helices and 58 β-strands across 6 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: 25 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	1
β-strand	20-26	7	1
β-strand	31	1	2
α-helix	32-42	11
α-helix	50-52	3
β-strand	53-57	5	1
β-strand	60	1	3
β-strand	63	1	3
α-helix	64-65	2
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	87-92	6	1
α-helix	104-110	7
α-helix	113-124	12
α-helix	128-137	10
α-helix	152-158	7
α-helix	163-171	9
α-helix	178	1
β-strand	179	1	4
α-helix	180	1
β-strand	185	1	4
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	286-292	7
α-helix	296-304	9
β-strand	312	1	5
β-strand	318	1	5
α-helix	319-326	8
α-helix	329-337	9
α-helix	340-342	3
α-helix	357-358	2

Chain B: 26 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	6
β-strand	20-26	7	6
β-strand	31	1	7
α-helix	32-42	11
α-helix	50-52	3
β-strand	53-57	5	6
β-strand	60	1	8
β-strand	63	1	8
α-helix	64-65	2
β-strand	66-67	2	6
α-helix	68-69	2
β-strand	73	1	7
α-helix	74-76	3
α-helix	78-80	3
β-strand	87-92	6	6
α-helix	104-110	7
α-helix	113-124	12
α-helix	128-137	10
α-helix	152-158	7
α-helix	163-171	9
α-helix	178	1
β-strand	179	1	9
α-helix	180	1
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	286-292	7
α-helix	296-304	9
β-strand	312	1	10
β-strand	318	1	10
α-helix	319-326	8
α-helix	329-337	9
α-helix	340-342	3
α-helix	349-351	3
α-helix	357-358	2

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	0-1	2
β-strand	2-10	9	1
α-helix	16-25	10
β-strand	38-46	9	1
β-strand	49-57	9	1
α-helix	65-74	10
β-strand	77-83	7	1
α-helix	87-104	18
β-strand	111-116	6	1
α-helix	128-137	10
β-strand	142-145	4	1
β-strand	147	1	11
β-strand	152	1	11
α-helix	154-166	13

Chains D and F: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	3
α-helix	16-25	10
β-strand	38-46	9	3
β-strand	49-57	9	3
α-helix	65-74	10
β-strand	77-83	7	3
α-helix	87-104	18
β-strand	111-116	6	3
α-helix	128-137	10
β-strand	142-145	4	3
β-strand	147	1	12
β-strand	152	1	12
α-helix	154-166	13

Chain E: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1	1
β-strand	2-9	8	6
α-helix	16-25	10
β-strand	38-46	9	6
β-strand	49-57	9	6
α-helix	65-74	10
β-strand	77-83	7	6
α-helix	87-104	18
β-strand	111-116	6	6
α-helix	128-137	10
β-strand	142-145	4	6
β-strand	147	1	13
β-strand	152	1	13
α-helix	154-166	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SH3 and multiple ankyrin repeat domains protein 3	A, B	protein	374	Mus musculus	Q4ACU6 (AlphaFold model)
Ras-related protein Rap-1b	C, D, E, F	protein	170	Homo sapiens	P61224 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6KYK_1 SH3 and multiple ankyrin repeat domains protein 3 (chains A, B)
GPGSEFMDGPGASAVVVRVGIPDLQQTKCLRLDPTAPVWAAKQRVLCALNHSLQDALNYG
LFQPPSRGRAGKFLDEERLLQDYPPNLDTPLPYLEFRYKRRVYAQNLIDDKQFAKLHTKA
NLKKFMDYVQLHSTDKVARLLDKGLDPNFHDPDSGECPLSLAAQLDNATDLLKVLRNGGA
HLDFRTRDGLTAVHCATRQRNAGALTTLLDLGASPDYKDSRGLTPLYHSALGGGDARCCE
LLLHDHAQLGTTDENGWQEIHQACRFGHVQHLEHLLFYGANMGAQNASGNTALHICALYN
QESCARVLLYRGANKDVRNYNSQTAFQVAIIAGNFELAEVIKTHKDSDVVPFRETPSYAK
RRRLAGPSGLASPR

Sequence of entity 2 (C, D, E, F), FASTA

>6KYK_2 Ras-related protein Rap-1b (chains C, D, E, F)
GPHMREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILD
TAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNK
CDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR

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
6KYH 3.3 Å, Crystal structure of Shank3 NTD-ANK A42K mutant in complex with HRas

Browse structure collections

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