PDB-5x2l: Crystal Structure of Human Serine Racemase

ID or keywords:

Entry

Database: PDB / ID: 5x2l

Title

Crystal Structure of Human Serine Racemase

Components

Serine racemase

Keywords

LYASE / ISOMERASE / Serine Racemase / PYRIDOXAL-5'-PHOSPHATE / human

Function / homology

Function and homology information

serine family amino acid metabolic process / D-serine biosynthetic process / serine racemase / threonine racemase activity / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / D-serine ammonia-lyase activity / L-serine ammonia-lyase activity / D-serine metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.806 Å

Authors

Obita, T. / Matsumoto, K. / Mori, H. / Toyooka, N. / Mizuguchi, M.

Citation

Journal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Design, synthesis, and evaluation of novel inhibitors for wild-type human serine racemase.
Authors: Takahara, S. / Nakagawa, K. / Uchiyama, T. / Yoshida, T. / Matsumoto, K. / Kawasumi, Y. / Mizuguchi, M. / Obita, T. / Watanabe, Y. / Hayakawa, D. / Gouda, H. / Mori, H. / Toyooka, N.

History

Deposition	Feb 1, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 24, 2021	Group: Derived calculations Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2	Apr 9, 2025	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5x2l.cif.gz	251.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5x2l.ent.gz	203 KB	Display	PDB format
PDBx/mmJSON format	5x2l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5x2l_validation.pdf.gz	460 KB	Display	wwPDB validaton report
Full document	5x2l_full_validation.pdf.gz	463.6 KB	Display
Data in XML	5x2l_validation.xml.gz	26.4 KB	Display
Data in CIF	5x2l_validation.cif.gz	37.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/5x2l ftp://data.pdbj.org/pub/pdb/validation_reports/x2/5x2l	HTTPS FTP

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Related structure data

Similar structure data	3vas-d 1p35-2 3wgm-d 6lhr-1 4dc3-d 6k1q-d 5j0a-d 2q6t-1 4bkm-2 3vaq-d 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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (3)

Deposited unit

A: Serine racemase

B: Serine racemase

hetero molecules

75.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	80.120, 112.590, 88.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Serine racemase / D-serine ammonia-lyase / D-serine dehydratase / L-serine ammonia-lyase / L-serine dehydratase Mass: 37674.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SRR / Production host: Escherichia coli (E. coli) References: UniProt: Q9GZT4, serine racemase, D-serine ammonia-lyase, L-serine ammonia-lyase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% PEG 8000, 5mM MgCl2, 10% Ethylene Glycol, 0.1M bis-Tris pH6.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 2, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.806→46.062 Å / Num. obs: 73388 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 9.1

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Resolution: 1.806→46.062 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.82

	R_factor	Num. reflection	% reflection
R_free	0.2581	3712	5.06 %
R_work	0.2201	-	-
obs	0.2221	73388	99.61 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.806→46.062 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4604	0	32	330	4966

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4729
X-RAY DIFFRACTION	f_angle_d	1.05	6419
X-RAY DIFFRACTION	f_dihedral_angle_d	14.941	1725
X-RAY DIFFRACTION	f_chiral_restr	0.043	768
X-RAY DIFFRACTION	f_plane_restr	0.005	819

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 (%)
1.806-1.8289	0.3498	137	0.3505	2566	X-RAY DIFFRACTION	99
1.8289-1.8529	0.3513	136	0.3277	2515	X-RAY DIFFRACTION	100
1.8529-1.8783	0.3557	150	0.3053	2538	X-RAY DIFFRACTION	100
1.8783-1.9052	0.3485	134	0.3104	2542	X-RAY DIFFRACTION	100
1.9052-1.9336	0.3506	146	0.2854	2520	X-RAY DIFFRACTION	99
1.9336-1.9638	0.2753	157	0.281	2522	X-RAY DIFFRACTION	99
1.9638-1.996	0.2805	143	0.2637	2541	X-RAY DIFFRACTION	99
1.996-2.0304	0.3041	137	0.2632	2551	X-RAY DIFFRACTION	100
2.0304-2.0673	0.3037	135	0.2569	2557	X-RAY DIFFRACTION	100
2.0673-2.1071	0.2805	161	0.2463	2549	X-RAY DIFFRACTION	100
2.1071-2.1501	0.2975	130	0.2291	2561	X-RAY DIFFRACTION	100
2.1501-2.1969	0.2655	122	0.2285	2588	X-RAY DIFFRACTION	100
2.1969-2.248	0.2287	118	0.2163	2555	X-RAY DIFFRACTION	100
2.248-2.3042	0.2799	111	0.2086	2604	X-RAY DIFFRACTION	100
2.3042-2.3665	0.2489	128	0.2077	2552	X-RAY DIFFRACTION	100
2.3665-2.4361	0.2893	143	0.2103	2586	X-RAY DIFFRACTION	100
2.4361-2.5147	0.2632	140	0.2146	2576	X-RAY DIFFRACTION	100
2.5147-2.6046	0.2533	131	0.2112	2562	X-RAY DIFFRACTION	100
2.6046-2.7089	0.2252	133	0.2187	2586	X-RAY DIFFRACTION	100
2.7089-2.8321	0.2592	145	0.2192	2586	X-RAY DIFFRACTION	100
2.8321-2.9814	0.2881	120	0.2264	2622	X-RAY DIFFRACTION	100
2.9814-3.1682	0.2811	141	0.2216	2585	X-RAY DIFFRACTION	100
3.1682-3.4127	0.2701	143	0.2136	2619	X-RAY DIFFRACTION	100
3.4127-3.756	0.2253	135	0.2068	2607	X-RAY DIFFRACTION	100
3.756-4.2992	0.2004	127	0.1776	2659	X-RAY DIFFRACTION	100
4.2992-5.4152	0.2154	145	0.1821	2673	X-RAY DIFFRACTION	100
5.4152-46.0765	0.2473	164	0.2251	2754	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	6.6654	-0.1997	4.4571	7.8197	0.0421	3.2043	-0.5488	0.0217	0.7315	0.1019	0.1751	0.3277	-1.2253	-0.3208	0.2744	0.2922	0.0548	0.1235	0.3397	0.0364	0.2645	-27.2216	-6.2868	-20.4523
2	2.9025	1.6458	-2.0555	4.0126	-2.8888	6.7089	-0.0156	-0.05	-0.1261	-0.1112	-0.1158	-0.2274	0.4564	0.3415	0.138	0.1506	-0.0046	-0.0164	0.1575	-0.0169	0.1838	-7.799	-15.0305	-27.6142
3	5.3606	3.7715	-2.6703	7.3979	-4.0858	4.9373	0.0976	-0.0276	0.1013	0.2595	0.0967	0.201	-0.1429	-0.3898	-0.1437	0.2223	-0.0312	-0.0024	0.281	0.0238	0.1772	-25.2536	-20.094	-12.7833
4	4.1331	-1.929	0.2591	7.7669	-1.492	3.6301	0.1238	0.2943	-0.4971	-0.1308	-0.367	0.2783	0.6874	0.1234	0.104	0.325	-0.0713	0.0109	0.3707	0.0455	0.243	-24.6922	-34.7766	-10.8376
5	4.4658	-1.149	1.4853	5.7609	-2.0648	3.9075	0.17	0.3234	-0.314	-0.7727	0.1617	0.8164	0.3647	-0.5605	-0.2791	0.438	-0.1116	-0.0601	0.4637	0.0019	0.3353	-34.5499	-33.5311	-13.1775
6	0.979	0.0728	-0.7152	1.389	-0.582	3.1644	-0.0477	0.1131	0.0212	-0.0704	0.1531	0.0055	-0.0074	-0.3877	-0.0855	0.2218	-0.0298	-0.015	0.2099	0.0288	0.2126	-23.1026	-13.378	-28.0633
7	4.7815	-0.7237	1.1301	3.7869	-0.014	2.0197	0.0266	0.1602	-0.4646	-0.4788	0.1615	0.4268	0.7078	-0.5777	-0.1288	0.3937	-0.2027	-0.0532	0.4208	0.0369	0.2572	-29.7117	-24.4678	-35.4439
8	2.1281	0.8242	1.5877	1.3452	0.7008	2.9974	0.1168	0.3729	-0.5058	-0.0926	0.0874	-0.0448	0.6429	0.1794	-0.189	0.3866	-0.0357	0.0421	0.2249	-0.0115	0.2413	-10.9206	-25.6068	-35.4889
9	2.2461	-0.1533	0.8611	0.3154	0.7647	2.6598	-0.0569	0.2543	-0.0784	-0.1455	0.0601	0.0062	0.2323	-0.0461	-0.0061	0.3007	-0.0771	0.0144	0.2002	-0.0313	0.2217	-11.4152	-19.0022	-35.221
10	8.7719	-3.5403	5.8911	8.1282	-3.909	4.3163	-0.4366	-0.2219	0.4375	0.099	0.3896	-0.5957	-0.7459	-0.0952	0.3418	0.2483	0.0289	0.0431	0.2734	-0.0557	0.3229	-56.0932	-6.2111	-21.7753
11	2.678	-0.2163	-1.5996	1.5429	0.2143	4.0712	0.0012	-0.1108	0.0429	0.2126	-0.0178	0.1047	0.0261	-0.1093	0.0444	0.2181	0.0247	-0.0101	0.1599	0.0023	0.2058	-76.5753	-14.3635	-17.8648
12	3.2927	-2.3827	-0.0925	6.5635	3.0851	2.3276	-0.0628	0.1466	0.1344	-0.2266	0.2225	-0.2778	-0.1261	0.4483	-0.1119	0.296	0.0309	0.0034	0.29	-0.0199	0.1748	-57.6797	-19.2152	-30.58
13	4.8771	0.1942	-0.2108	5.826	1.4426	4.4839	0.0736	-0.1135	-0.2439	0.3669	0.0602	-0.2679	0.2437	0.3356	-0.0917	0.3374	0.0738	-0.0127	0.3052	-0.0323	0.1918	-56.9245	-31.4192	-32.2041
14	1.0742	-0.0608	-0.5876	1.0136	0.6387	2.0907	-0.1213	-0.1036	0.0192	0.0972	0.142	-0.1149	0.1002	0.259	-0.0385	0.2643	0.0718	-0.0366	0.1953	-0.0298	0.2269	-62.2917	-13.5879	-15.8803
15	3.346	-0.1634	0.3841	1.4281	0.1012	1.7261	0.1225	-0.1035	-0.6163	0.2806	0.171	-0.5181	0.8482	0.5422	-0.0662	0.6089	0.2378	-0.0789	0.4678	0.0064	0.3737	-56.3922	-28.2376	-6.1524
16	1.8069	0.3433	-0.6976	1.2755	-0.2806	2.2467	-0.0974	-0.0252	-0.0836	0.3709	0.2119	-0.22	0.3284	0.5043	-0.0467	0.3492	0.1572	-0.0752	0.3021	-0.0294	0.2621	-58.0998	-20.1433	-9.0191
17	4.6148	-2.3128	3.5694	3.3839	-2.113	4.8054	-0.0235	-0.5999	-0.4569	0.1934	0.1834	0.1083	0.9643	-0.5417	-0.0464	0.4534	-0.0258	0.0184	0.2354	0.0313	0.2841	-79.2579	-28.3201	-10.9595
18	1.8393	-0.4666	0.2993	0.8671	-0.2323	2.477	-0.1733	-0.1136	-0.2057	0.0529	0.0204	-0.1539	0.8502	0.0833	-0.0334	0.3905	0.042	0.0007	0.1501	0.0329	0.2653	-75.4348	-23.9983	-13.518
19	1.6824	-0.3662	-0.0256	1.3879	0.2091	3.7772	-0.1909	-0.2853	0.0239	0.2224	0.1487	-0.0022	-0.3535	-0.1609	0	0.2995	0.0981	-0.0205	0.2493	-0.0062	0.2166	-73.1329	-16.12	-5.8124

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 54 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 55 through 98 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 99 through 120 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 121 through 145 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 146 through 214 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 215 through 255 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 256 through 278 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 279 through 317 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 19 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 20 through 54 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 55 through 85 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 86 through 145 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 146 through 214 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 215 through 237 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 238 through 263 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 264 through 278 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 279 through 294 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 295 through 317 )

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