PDB-4g1c: Human SIRT5 bound to Succ-IDH2 and Carba-NAD

ID or keywords:

Entry

Database: PDB / ID: 4g1c

Title

Human SIRT5 bound to Succ-IDH2 and Carba-NAD

Components

NAD-dependent protein deacylase sirtuin-5, mitochondrial
Succinylated IDH2 peptide

Keywords

HYDROLASE / Sirtuin / Succinylated peptide / CarbaNAD

Function / homology

Function and homology information

protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.944 Å

Authors

Dai, H.

Citation

Journal: J.Org.Chem. / Year: 2012
Title: Synthesis of Carba-NAD and the Structures of Its Ternary Complexes with SIRT3 and SIRT5.
Authors: Szczepankiewicz, B.G. / Dai, H. / Koppetsch, K.J. / Qian, D. / Jiang, F. / Mao, C. / Perni, R.B.

History

Deposition	Jul 10, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 19, 2012	Group: Database references
Revision 1.2	Mar 26, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4g1c.cif.gz	231.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4g1c.ent.gz	185.8 KB	Display	PDB format
PDBx/mmJSON format	4g1c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g1/4g1c ftp://data.pdbj.org/pub/pdb/validation_reports/g1/4g1c	HTTPS FTP

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Related structure data

Related structure data	4fvtC C: citing same article (ref.)
Similar structure data	6ljk-d 2b4y-2 4hda-2 4f4u-1 2b4y-4 2b4y-3 5xhs-d 2nyr-2 6enx-d 5bwl-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#213 - Sep 2017 Sirtuins similarity (7) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: NAD-dependent protein deacylase sirtuin-5, mitochondrial

B: NAD-dependent protein deacylase sirtuin-5, mitochondrial

D: Succinylated IDH2 peptide

E: Succinylated IDH2 peptide

hetero molecules

60.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NAD-dependent protein deacylase sirtuin-5, mitochondrial

D: Succinylated IDH2 peptide

hetero molecules

defined by author&software
30.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NAD-dependent protein deacylase sirtuin-5, mitochondrial

E: Succinylated IDH2 peptide

hetero molecules

defined by author&software
29.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	67.239, 84.425, 95.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NAD-dependent protein deacylase sirtuin-5, mitochondrial / Regulatory protein SIR2 homolog 5 / SIR2-like protein 5 Mass: 29054.121 Da / Num. of mol.: 2 / Fragment: UNP residues 36-302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5, SIR2L5 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide	Succinylated IDH2 peptide Mass: 614.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic Succ-IDH2 peptide
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₃₀N₇O₁₃P₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.28 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.15 M magnesium formate, and 20% (w/v) PEG 3350, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2011
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.94→50 Å / Num. all: 40594 / Num. obs: 40594 / % possible obs: 99.8 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 19.8
Reflection shell	Resolution: 1.94→2.02 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.2_869)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.944→35.402 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 25.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2418	2037	5.02 %	RANDOM
R_work	0.1944	-	-	-
all	0.1969	40594	-	-
obs	0.1969	40594	99.46 %	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.358 Å² / k_sol: 0.342 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.2318 Å²	-0 Å²	-0 Å²
2-	-	0.0879 Å²	-0 Å²
3-	-	-	-0.3197 Å²

Refinement step

Cycle: LAST / Resolution: 1.944→35.402 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4162	0	46	225	4433

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4401
X-RAY DIFFRACTION	f_angle_d	1.178	5986
X-RAY DIFFRACTION	f_dihedral_angle_d	14.86	1606
X-RAY DIFFRACTION	f_chiral_restr	0.085	647
X-RAY DIFFRACTION	f_plane_restr	0.006	788

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9438-1.989	0.3113	123	0.2695	2403	X-RAY DIFFRACTION	94
1.989-2.0387	0.3308	135	0.2496	2552	X-RAY DIFFRACTION	100
2.0387-2.0938	0.2889	131	0.2262	2546	X-RAY DIFFRACTION	100
2.0938-2.1555	0.3052	111	0.2239	2568	X-RAY DIFFRACTION	100
2.1555-2.225	0.2611	129	0.2101	2538	X-RAY DIFFRACTION	100
2.225-2.3045	0.2717	129	0.2105	2565	X-RAY DIFFRACTION	100
2.3045-2.3968	0.2389	139	0.2095	2580	X-RAY DIFFRACTION	100
2.3968-2.5058	0.2396	150	0.2052	2540	X-RAY DIFFRACTION	100
2.5058-2.6379	0.2734	134	0.2124	2551	X-RAY DIFFRACTION	100
2.6379-2.8031	0.2756	140	0.2212	2579	X-RAY DIFFRACTION	100
2.8031-3.0194	0.3129	131	0.2164	2588	X-RAY DIFFRACTION	100
3.0194-3.3231	0.2803	158	0.2123	2575	X-RAY DIFFRACTION	100
3.3231-3.8035	0.2197	136	0.1865	2611	X-RAY DIFFRACTION	100
3.8035-4.7901	0.186	146	0.1581	2635	X-RAY DIFFRACTION	100
4.7901-35.4083	0.2111	145	0.1676	2726	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0215	-0.0025	0.0055	0.0088	-0.0107	0.0121	-0.026	0.029	-0.0167	-0.0744	-0.0452	0.047	-0.0077	-0.0307	-0.033	0.4452	0.0655	-0.2903	0.305	-0.1783	0.3827	29.3576	-9.7214	5.5909
2	0.014	-0.0085	-0.0047	0.0088	-0.0024	0.0916	0.0011	0.004	0.0082	-0.0122	0.0473	0.2516	0.0068	-0.0398	0.0122	0.1444	-0.048	-0.0165	0.1931	0.0435	0.2987	23.9622	0.9076	20.2323
3	0.0399	0.0611	-0.0254	0.075	-0.0363	0.0155	-0.1466	-0.1784	-0.1975	0.1848	-0.0867	0.232	0.1527	-0.1704	-0.1214	0.044	-0.0309	0.4769	0.2914	0.0231	0.122	15.6869	15.4717	33.2148
4	0.0509	0.1057	0.1381	0.2634	0.2501	0.4512	0.1192	0.0582	-0.0543	0.0845	0.1346	0.2	0.0808	0.0141	0.1776	0.2006	-0.058	-0.0172	0.1161	0.0729	0.3254	30.4182	-9.0847	23.7715
5	0.0191	-0.0149	-0.003	0.0138	0.0039	0.0353	0.0225	-0.0301	-0.0329	0.0745	0.0467	0.089	0.0225	-0.0194	0.0774	0.2003	-0.05	0.0122	0.1518	0.0653	0.1775	31.0411	0.104	24.5729
6	0.0714	-0.0279	-0.0066	0.0164	-0.0135	0.0407	-0.0778	-0.0354	0.0044	0.2114	0.0441	-0.0777	-0.0404	-0.0488	-0.0548	0.2512	0.008	-0.0181	0.1828	0.0477	0.127	32.1771	10.1091	32.9358
7	-0.0002	-0.002	-0.0143	-0.0067	-0.0007	0.0028	-0.0789	-0.1223	-0.0408	0.2443	0.0072	0.1356	-0.0212	-0.1783	-0.0271	0.6139	0.0956	0.3309	0.5706	0.1612	0.0736	18.2636	15.1454	44.0421
8	0.0056	-0.0435	0.0156	0.1107	-0.0554	0.0255	-0.0109	-0.0718	0.0149	-0.0068	0.0096	-0.0881	-0.0726	0.091	0	0.1892	-0.0034	-0.0374	0.1884	0.0339	0.161	31.722	12.2386	22.534
9	0.0124	0.0312	0.0273	0.1407	0.0528	0.0742	0.0679	0.064	0.0434	-0.2622	-0.0983	0.072	0.0425	-0.0715	-0.0493	0.2789	0.0048	-0.084	0.1878	0.0359	0.1773	26.832	4.8095	8.9474
10	0.0203	-0.0009	-0.0051	0.0419	0.0186	0.052	0.0225	0.1059	-0.1393	-0.0494	-0.1535	0.1633	-0.0203	-0.133	-0.0756	0.331	-0.0093	-0.289	0.2561	-0.0647	0.4617	22.8831	-4.4806	10.1704
11	0.0142	-0.0291	0.0167	0.063	-0.0342	0.0359	-0.0452	-0.1075	0.019	0.0974	-0.0389	0.0681	-0.1566	-0.1201	0.0229	0.1819	0.3424	-0.1703	0.4398	-0.3494	0.4703	5.7053	42.8776	24.7968
12	0.3893	-0.0458	0.3692	0.0083	-0.0497	0.3559	-0.0113	-0.2815	0.1106	0.248	-0.046	0.3917	0.0925	-0.2444	0.0079	0.3747	0.0329	-0.0827	0.2542	-0.0637	0.4118	11.2869	15.0141	9.3279
13	0.0039	0.0062	0.0062	0.0093	0.0107	0.0313	-0.052	-0.0125	0.0395	-0.0962	-0.0541	0.075	0.0296	-0.0392	-0.0731	0.3852	0.1284	-0.4561	0.2967	-0.1138	0.3012	7.3494	20.2155	1.2993
14	0.0246	0.0023	0.0107	0.0053	-0.0007	0.0016	0.0429	0.0132	-0.026	-0.0052	0.0443	0.0538	-0.0433	-0.0429	0.055	0.2449	0.5415	-0.4714	0.6561	-0.3041	0.77	1.1128	43.335	13.0254
15	0.0165	-0.0008	0.0141	0.0072	-0.0124	0.028	0.0247	-0.0063	0.0195	-0.0423	-0.0271	0.0276	-0.0908	-0.0815	0.0469	0.2648	0.3002	-0.4143	0.3884	-0.2191	0.4495	8.6809	40.2468	11.8196
16	0.0257	0.0086	0.0484	0.046	0.0046	0.1974	-0.1618	0.1323	0.0253	-0.4461	-0.0997	0.1949	0.1944	-0.1375	-0.3358	0.2476	0.2456	-0.5779	0.2336	0.0623	-0.0645	12.8901	24.2735	-3.2995
17	0.0079	-0.016	0.0133	0.1122	-0.036	0.0206	-0.0405	-0.016	0.101	-0.1315	-0.0403	0.1159	-0.1183	-0.045	-0.0729	0.226	0.0296	-0.0919	0.308	-0.0195	0.2455	18.9678	34.8919	15.8997
18	0.0605	0.0013	0.01	0.0189	0.0256	0.0453	-0.0434	-0.1194	-0.0169	0.0106	-0.0704	0.0943	-0.0083	-0.1373	-0.0712	0.0474	0.1688	-0.1451	0.3735	-0.1306	0.2578	13.6523	35.2388	27.2855
19	0.0338	-0.0048	-0.0227	0.0013	0.0033	0.0134	-0.0138	-0.0394	0.0286	0.0499	-0.0733	0.059	-0.0232	-0.0595	-0.0308	0.1217	0.1983	-0.0544	0.7623	-0.2111	0.562	3.3246	37.8502	27.9376
20	0.0064	-0.0006	-0.0007	0.0039	0.001	0.0012	-0.0023	-0.0062	-0.0093	-0.0355	-0.0179	0.016	-0.0187	-0.0213	0	0.2396	0.017	-0.0081	0.2467	0.0302	0.1911	25.3751	18.2232	19.8622
21	0.0004	0.0001	-0.0024	0.006	-0.0104	0.025	-0.0102	0.0244	-0.0011	0.0056	-0.0412	0.0015	0.0088	-0.0023	-0.0161	0.1833	0.0581	-0.0977	0.2876	-0.0169	0.3192	21.2888	24.6203	15.8465

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 36:49)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 50:71)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 72:111)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 112:131)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 132:149)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 150:174)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 175:209)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 210:256)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 257:281)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 282:302)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 36:65)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 66:94)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 95:111)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 112:130)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 131:149)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 150:218)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 219:256)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 257:281)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 282:302)
20	X-RAY DIFFRACTION	20	chain 'D'
21	X-RAY DIFFRACTION	21	chain 'E'

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