A0A087WZ12_HUMAN Loading...

Methyl-CpG binding domain protein 3

AlphaFold DB , UniProt , Accession A0A087WZ12, Species HUMAN (Homo sapiens, Human), Gene MBD3, Length 34 aa.

						>A0A087WZ12_HUMAN|A0A087WZ12|MBD3
MDLSTFDFRTGKMLMSKMNKSRQRVRYDSSNQVK
					

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(Predicted Aligned Error values between residue pairs)

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Site	Residue	pLDDT	pLDDT confidence	pLDDT₁₀	pLDDT10 confidence	SASA	SASA [Å²]	SASA₁₀	SASA10 [Å²]	RSA	RSA unformatted	RSA₁₀	RSA10 unformatted	Surface	Surface10 (not used)	Disorder (not used)	Disorder	Sec. str.	Secondary structure	Isomer	Phi (φ)	Psi (ψ)	Omega (ω)	Chi 1 (χ₁)	Chi 2 (χ₂)	Chi 3 (χ₃)	Chi 4 (χ₄)	Chi 5 (χ₅)	Tau (τ)	Contacts (colored by PAE)	Contact details
1	M	74	Confident	86.5	Confident	211 Å²	211	107.4 Å²	107.4	100%	1.039	55%	0.552	S	S	*	*				0	107.3	0	-179.6	-176	-80.8	0	0	106.8	L3	M1-L3 HydrophobicContact CG-CG 4.09Å; M1-L3 PolarHBondContact O-N 3.5Å; M1-L3 HydrophobicContact SD-CD1 4.48Å; M1-L3 HydrophobicContact SD-CD2 3.72Å; M1-L3 HydrophobicContact SD-CG 4.26Å; M1-L3 HydrophobicContact CG-CD2 3.75Å
2	D	78.4	Confident	86.8	Confident	121 Å²	121	110.5 Å²	110.5	65%	0.647	56%	0.559	S	S	*	*			trans	-84	105.3	178.6	-177.5	1.3	0	0	0	109.6	S4	D2-S4 PolarHBondContact OD2-OG 3.41Å; D2-S4 PolarHBondContact OD1-OG 3.32Å; D2-S4 PolarHBondContact OD1-N 3.19Å; D2-S4 WeakPolarHBondContact OD1-CB 3.28Å; D2-S4 VanDerWaalsContact CG-OG 3.22Å; D2-S4 VanDerWaalsContact C-N 3.33Å
3	L	85.4	Confident	87	Confident	79 Å²	79	109.6 Å²	109.6	41%	0.414	55%	0.553	S	S	.	*			trans	-91.2	9.1	-179.5	-63.9	178.4	0	0	0	112.8	M1 T5 F6	M1-L3 HydrophobicContact CG-CG 4.09Å; M1-L3 PolarHBondContact O-N 3.5Å; M1-L3 HydrophobicContact SD-CD1 4.48Å; M1-L3 HydrophobicContact SD-CD2 3.72Å; M1-L3 HydrophobicContact SD-CG 4.26Å; M1-L3 HydrophobicContact CG-CD2 3.75Å; L3-T5 PolarHBondContact O-N 3.12Å; L3-F6 HydrophobicContact CB-CB 4.26Å; L3-F6 HydrophobicContact CD2-CB 4.11Å; L3-F6 HydrophobicContact CD2-CG 4.47Å; L3-F6 WeakPolarHBondContact O-CB 3.46Å; L3-F6 PolarHBondContact O-N 3.16Å
4	S	84.6	Confident	86.7	Confident	79 Å²	79	108.2 Å²	108.2	55%	0.552	55%	0.547	S	S	*	.	T	Hydrogen-bonded Turn	trans	-59.5	-16.4	-180	63.2	0	0	0	0	114.5	D2	D2-S4 PolarHBondContact OD2-OG 3.41Å; D2-S4 PolarHBondContact OD1-OG 3.32Å; D2-S4 PolarHBondContact OD1-N 3.19Å; D2-S4 WeakPolarHBondContact OD1-CB 3.28Å; D2-S4 VanDerWaalsContact CG-OG 3.22Å; D2-S4 VanDerWaalsContact C-N 3.33Å
5	T	84.6	Confident	85.5	Confident	39 Å²	39	110.1 Å²	110.1	24%	0.239	56%	0.556	C	S	.	*	T	Hydrogen-bonded Turn	trans	-107.7	-1.3	175.1	62	0	0	0	0	113.5	L3 M13 L14 K17	L3-T5 PolarHBondContact O-N 3.12Å; T5-M13 CarbonylContact O-C 3.58Å; T5-M13 VanDerWaalsContact OG1-CE 3.3Å; T5-M13 WeakPolarHBondContact OG1-CE 3.37Å; T5-L14 VanDerWaalsContact O-CB 3.29Å; T5-L14 PolarHBondContact O-N 3.31Å; T5-L14 WeakPolarHBondContact O-CB 3.49Å; T5-K17 HydrophobicContact CG2-CB 4.35Å; T5-K17 HydrophobicContact CG2-CD 4.25Å
6	F	91.9	Very high	84.3	Confident	68 Å²	68	108.8 Å²	108.8	30%	0.298	56%	0.56	S	S	.	*	E	Extended strand (participates in β ladder)	trans	-83.3	130.6	178	-173	-104	0	0	0	110.8	L3 F8 G11 M13	L3-F6 HydrophobicContact CB-CB 4.26Å; L3-F6 HydrophobicContact CD2-CB 4.11Å; L3-F6 HydrophobicContact CD2-CG 4.47Å; L3-F6 WeakPolarHBondContact O-CB 3.46Å; L3-F6 PolarHBondContact O-N 3.16Å; F6-F8 HydrophobicContact CE1-CD1 3.94Å; F6-F8 HydrophobicContact CE1-CG 4.37Å; F6-F8 HydrophobicContact CE1-CE1 4.07Å; F6-F8 AromaticContact CE1-CD1 3.94Å; F6-F8 HydrophobicContact CD1-CZ 4.09Å; F6-F8 HydrophobicContact CD1-CG 4.27Å; F6-F8 HydrophobicContact CD1-CE2 4.24Å; F6-F8 HydrophobicContact CD1-CE1 4.02Å; F6-F8 HydrophobicContact CD1-CD2 4.33Å; F6-F8 HydrophobicContact CD1-CD1 4.11Å; F6-G11 WeakPolarHBondContact CE2-O 3.27Å; F6-M13 HydrophobicContact CB-SD 3.79Å; F6-M13 HydrophobicContact CD2-CG 4.31Å; F6-M13 HydrophobicContact CD2-SD 3.68Å; F6-M13 HydrophobicContact CG-SD 4.23Å
7	D	88.4	Confident	82.9	Confident	63 Å²	63	110.3 Å²	110.3	34%	0.337	56%	0.561	S	S	.	*	E	Extended strand (participates in β ladder)	trans	-97.1	113.9	175.6	179.5	-0.2	0	0	0	110.2	R9 T10 G11 K12	D7-R9 VanDerWaalsContact C-N 3.33Å; D7-R9 PolarHBondContact OD1-N 3.43Å; D7-R9 PolarHBondContact O-N 3.47Å; D7-R9 WeakPolarHBondContact OD1-CB 3.38Å; D7-T10 WeakPolarHBondContact CB-OG1 3.42Å; D7-T10 PolarHBondContact O-N 3.47Å; D7-T10 WeakPolarHBondContact OD2-CG2 3.29Å; D7-T10 PolarHBondContact OD2-OG1 2.76Å; D7-G11 VanDerWaalsContact O-CA 3.27Å; D7-G11 WeakPolarHBondContact O-CA 3.35Å; D7-G11 PolarHBondContact O-N 2.87Å; D7-K12 PolarHBondContact N-O 3.02Å; D7-K12 PolarHBondContact O-N 3.08Å; D7-K12 WeakPolarHBondContact CB-O 3.39Å
8	F	91.2	Very high	81.6	Confident	164 Å²	164	112.4 Å²	112.4	72%	0.719	57%	0.571	S	S	*	*	T	Hydrogen-bonded Turn	trans	-71	-25.5	178.9	-70.8	-83.8	0	0	0	113.9	F6	F6-F8 HydrophobicContact CE1-CD1 3.94Å; F6-F8 HydrophobicContact CE1-CG 4.37Å; F6-F8 HydrophobicContact CE1-CE1 4.07Å; F6-F8 AromaticContact CE1-CD1 3.94Å; F6-F8 HydrophobicContact CD1-CZ 4.09Å; F6-F8 HydrophobicContact CD1-CG 4.27Å; F6-F8 HydrophobicContact CD1-CE2 4.24Å; F6-F8 HydrophobicContact CD1-CE1 4.02Å; F6-F8 HydrophobicContact CD1-CD2 4.33Å; F6-F8 HydrophobicContact CD1-CD1 4.11Å
9	R	91.1	Very high	80.5	Confident	235 Å²	235	111.3 Å²	111.3	89%	0.887	57%	0.567	S	S	*	*	T	Hydrogen-bonded Turn	trans	-71.3	-36.6	178.3	176.6	179.2	-80.8	172.1	-5.9	111	D7	D7-R9 VanDerWaalsContact C-N 3.33Å; D7-R9 PolarHBondContact OD1-N 3.43Å; D7-R9 PolarHBondContact O-N 3.47Å; D7-R9 WeakPolarHBondContact OD1-CB 3.38Å
10	T	91	Very high	79.5	Confident	76 Å²	76	114.3 Å²	114.3	47%	0.466	58%	0.575	S	S	.	*	T	Hydrogen-bonded Turn	trans	-110.1	-12.9	-174.1	64.3	0	0	0	0	114.3	D7 K12	D7-T10 WeakPolarHBondContact CB-OG1 3.42Å; D7-T10 PolarHBondContact O-N 3.47Å; D7-T10 WeakPolarHBondContact OD2-CG2 3.29Å; D7-T10 PolarHBondContact OD2-OG1 2.76Å; T10-K12 PolarHBondContact O-N 3.39Å
11	G	91.4	Very high	78.4	Confident	46 Å²	46	113.6 Å²	113.6	47%	0.474	58%	0.581	S	S	.	*	T	Hydrogen-bonded Turn	trans	69.9	18.2	-175.3	0	0	0	0	0	113.8	F6 D7	F6-G11 WeakPolarHBondContact CE2-O 3.27Å; D7-G11 VanDerWaalsContact O-CA 3.27Å; D7-G11 WeakPolarHBondContact O-CA 3.35Å; D7-G11 PolarHBondContact O-N 2.87Å
12	K	89.3	Confident	77.6	Confident	145 Å²	145	112.5 Å²	112.5	63%	0.63	57%	0.565	S	S	*	*	E	Extended strand (participates in β ladder)	trans	-114.1	147.2	-173.7	-65	-176.9	-179.2	-178.1	0	111.7	D7 T10	D7-K12 PolarHBondContact N-O 3.02Å; D7-K12 PolarHBondContact O-N 3.08Å; D7-K12 WeakPolarHBondContact CB-O 3.39Å; T10-K12 PolarHBondContact O-N 3.39Å
13	M	89.3	Confident	76.6	Confident	99 Å²	99	112.7 Å²	112.7	49%	0.488	56%	0.562	S	S	.	*	E	Extended strand (participates in β ladder)	trans	-76	128.1	168.8	-65	-69.7	-84	0	0	109.6	T5 F6 M15	T5-M13 CarbonylContact O-C 3.58Å; T5-M13 VanDerWaalsContact OG1-CE 3.3Å; T5-M13 WeakPolarHBondContact OG1-CE 3.37Å; F6-M13 HydrophobicContact CB-SD 3.79Å; F6-M13 HydrophobicContact CD2-CG 4.31Å; F6-M13 HydrophobicContact CD2-SD 3.68Å; F6-M13 HydrophobicContact CG-SD 4.23Å; M13-M15 VanDerWaalsContact C-N 3.31Å; M13-M15 VanDerWaalsContact O-CG 3.28Å; M13-M15 WeakPolarHBondContact O-CG 3.05Å; M13-M15 PolarHBondContact O-N 3.33Å
14	L	83.1	Confident	75.2	Confident	90 Å²	90	119.9 Å²	119.9	47%	0.471	58%	0.584	S	S	.	*			trans	-71.4	83.1	177.5	-174.2	63.9	0	0	0	110.3	T5 S16 K17	T5-L14 VanDerWaalsContact O-CB 3.29Å; T5-L14 PolarHBondContact O-N 3.31Å; T5-L14 WeakPolarHBondContact O-CB 3.49Å; L14-S16 PolarHBondContact O-N 3.48Å; L14-S16 VanDerWaalsContact O-N 3.08Å; L14-K17 HydrophobicContact CD2-CD 4.27Å; L14-K17 PolarHBondContact O-N 2.72Å; L14-K17 HydrophobicContact CD2-CG 4.33Å
15	M	69.5	Low	73.8	Confident	136 Å²	136	121.8 Å²	121.8	67%	0.67	59%	0.592	S	S	*	*	G	3₁₀ helix	trans	-61.4	-19.7	-176.8	-47	-164.9	83.8	0	0	113.7	M13 K17 M18 N19	M13-M15 VanDerWaalsContact C-N 3.31Å; M13-M15 VanDerWaalsContact O-CG 3.28Å; M13-M15 WeakPolarHBondContact O-CG 3.05Å; M13-M15 PolarHBondContact O-N 3.33Å; M15-K17 VanDerWaalsContact C-N 3.28Å; M15-K17 PolarHBondContact O-N 2.84Å; M15-M18 WeakPolarHBondContact O-CB 3.3Å; M15-M18 PolarHBondContact O-N 3.48Å; M15-N19 PolarHBondContact O-N 2.77Å
16	S	65.3	Low	72.6	Confident	90 Å²	90	129.5 Å²	129.5	63%	0.629	62%	0.617	S	S	*	*	G	3₁₀ helix	trans	-58	-37.1	178.4	178.7	0	0	0	0	112.8	L14 M18	L14-S16 PolarHBondContact O-N 3.48Å; L14-S16 VanDerWaalsContact O-N 3.08Å; S16-M18 VanDerWaalsContact C-N 3.31Å; S16-M18 PolarHBondContact O-N 2.86Å
17	K	60.7	Low	70.9	Confident	134 Å²	134	135.3 Å²	135.3	58%	0.583	64%	0.638	S	S	*	*	G	3₁₀ helix	trans	-73.7	-23.2	176.2	-72.9	-178.1	178.5	173.8	0	112.9	T5 L14 M15 N19	T5-K17 HydrophobicContact CG2-CB 4.35Å; T5-K17 HydrophobicContact CG2-CD 4.25Å; L14-K17 HydrophobicContact CD2-CD 4.27Å; L14-K17 PolarHBondContact O-N 2.72Å; L14-K17 HydrophobicContact CD2-CG 4.33Å; M15-K17 VanDerWaalsContact C-N 3.28Å; M15-K17 PolarHBondContact O-N 2.84Å; K17-N19 VanDerWaalsContact C-N 3.35Å
18	M	60	Low	69.4	Low	148 Å²	148	139.6 Å²	139.6	73%	0.729	66%	0.661	S	S	*	*	G	3₁₀ helix	trans	-78.7	-19.2	179.7	-146.3	175.3	82.7	0	0	112.7	M15 S16	M15-M18 WeakPolarHBondContact O-CB 3.3Å; M15-M18 PolarHBondContact O-N 3.48Å; S16-M18 VanDerWaalsContact C-N 3.31Å; S16-M18 PolarHBondContact O-N 2.86Å
19	N	60.7	Low	67.7	Low	92 Å²	92	137 Å²	137	49%	0.492	66%	0.664	S	S	.	*	S	Bend	trans	-93.9	-9.3	-175.2	-145.6	-22.9	0	0	0	114.3	M15 K17 S21 R22 Q23	M15-N19 PolarHBondContact O-N 2.77Å; K17-N19 VanDerWaalsContact C-N 3.35Å; N19-S21 PolarHBondContact O-N 2.91Å; N19-S21 VanDerWaalsContact O-N 3.16Å; N19-R22 PolarHBondContact O-N 3Å; N19-R22 VanDerWaalsContact O-N 3.12Å; N19-Q23 PolarHBondContact O-N 2.71Å
20	K	60.4	Low	66	Low	171 Å²	171	130.4 Å²	130.4	74%	0.743	65%	0.653	S	S	*	*	H	α-helix	trans	-61.9	-21.2	173.1	-90.5	-179	173.3	175.7	0	113.4
21	S	56.6	Low	64.4	Low	99 Å²	99	134.2 Å²	134.2	69%	0.692	67%	0.671	S	S	*	*	H	α-helix	trans	-75.3	-29.8	175.7	178.7	0	0	0	0	113.2	N19	N19-S21 PolarHBondContact O-N 2.91Å; N19-S21 VanDerWaalsContact O-N 3.16Å
22	R	57.6	Low	62.8	Low	188 Å²	188	141.1 Å²	141.1	71%	0.709	69%	0.691	S	S	*	*	H	α-helix	trans	-93.9	-20.2	-176.3	-84.2	-177.8	176.6	-172.6	-0.4	115	N19	N19-R22 PolarHBondContact O-N 3Å; N19-R22 VanDerWaalsContact O-N 3.12Å
23	Q	57.5	Low	60.8	Low	125 Å²	125	140.7 Å²	140.7	58%	0.584	70%	0.7	S	S	*	*	H	α-helix	trans	-80.9	-20.3	178	-85	-169.1	-32.8	0	0	114.2	N19 V25 R26	N19-Q23 PolarHBondContact O-N 2.71Å; Q23-V25 PolarHBondContact O-N 3.15Å; Q23-R26 PolarHBondContact O-N 2.91Å
24	R	55.3	Low	58.7	Low	230 Å²	230	148.7 Å²	148.7	87%	0.868	73%	0.732	S	S	*	*	T	Hydrogen-bonded Turn	trans	-69.9	-13	-178	-151.5	175.2	174.5	-170.8	-2.9	113.9
25	V	54.9	Low	57.5	Low	119 Å²	119	151.7 Å²	151.7	72%	0.721	75%	0.745	S	S	*	*	T	Hydrogen-bonded Turn	trans	-99.3	-14.9	179.3	-172.1	0	0	0	0	112.7	Q23	Q23-V25 PolarHBondContact O-N 3.15Å
26	R	60.5	Low	56.9	Low	202 Å²	202	152.5 Å²	152.5	76%	0.762	75%	0.749	S	S	*	*	S	Bend	trans	-104.9	8.6	-171.5	-87	-166.3	177.4	108.7	-2.2	116	Q23	Q23-R26 PolarHBondContact O-N 2.91Å
27	Y	55.3	Low	56.4	Low	189 Å²	189	155.9 Å²	155.9	74%	0.741	76%	0.756	S	S	*	*	S	Bend	trans	-119.5	2.6	177.5	-97.2	-81.1	0	0	0	115.7	S29	Y27-S29 VanDerWaalsContact C-N 3.35Å; Y27-S29 PolarHBondContact O-N 3.39Å
28	D	56.6	Low	56.1	Low	154 Å²	154	157.2 Å²	157.2	82%	0.824	77%	0.766	S	S	*	*	T	Hydrogen-bonded Turn	trans	-95.1	24	177.1	-161.1	25.5	0	0	0	114.1
29	S	55.6	Low	55.9	Low	110 Å²	110	157.8 Å²	157.8	77%	0.769	77%	0.768	S	S	*	*	T	Hydrogen-bonded Turn	trans	-140.6	32	177.2	28.4	0	0	0	0	113.3	Y27	Y27-S29 VanDerWaalsContact C-N 3.35Å; Y27-S29 PolarHBondContact O-N 3.39Å
30	S	55.7	Low	55.6	Low	96 Å²	96	162.2 Å²	162.2	67%	0.671	79%	0.786	S	S	*	*	S	Bend	trans	-133.2	45.3	171.2	-156.5	0	0	0	0	112.3
31	N	56.8	Low	55.2	Low	155 Å²	155	161.6 Å²	161.6	83%	0.829	79%	0.789	S	S	*	*	S	Bend	trans	-145.4	24.6	167.5	-128.1	17.7	0	0	0	114.7
32	Q	58.6	Low	55.1	Low	192 Å²	192	166.4 Å²	166.4	90%	0.897	80%	0.797	S	S	*	*			trans	-121	67.7	166.2	-67.7	-72.5	-17.5	0	0	107.8
33	V	46.8	Very low	54.9	Low	135 Å²	135	164.6 Å²	164.6	82%	0.818	80%	0.804	S	S	*	*			trans	-97.9	116.6	160.5	-175.9	0	0	0	0	105.8
34	K	45.6	Very low	54.7	Low	268 Å²	268	168.2 Å²	168.2	100%	1.165	82%	0.824	S	S	*	*			trans	-36.3	0	175.6	178.3	176.5	174	-75.8	0	115.7

Retrieved 34 of 34 residues in 315.9 ms (Link to these results)

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