PDB-4djo: Crystal Structure of wild-type HIV-1 Protease in Complex with MKP56

ID or keywords:

Entry

Database: PDB / ID: 4djo

Title

Crystal Structure of wild-type HIV-1 Protease in Complex with MKP56

Components

Pol polyprotein

Keywords

HYDROLASE/HYDROLASE inhibitor / HIV-1 protease / drug resistance / drug design / Protease inhibitors / AIDS / Aspartyl protease / HYDROLASE-HYDROLASE inhibitor complex

Function / homology

Function and homology information

viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Schiffer, C.A. / Nalam, M.N.L.

Citation

Journal: J.Med.Chem. / Year: 2012
Title: Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance.
Authors: Parai, M.K. / Huggins, D.J. / Cao, H. / Nalam, M.N. / Ali, A. / Schiffer, C.A. / Tidor, B. / Rana, T.M.

History

Deposition	Feb 2, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 1, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 2, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4djo.cif.gz	104 KB	Display	PDBx/mmCIF format
PDB format	pdb4djo.ent.gz	83.5 KB	Display	PDB format
PDBx/mmJSON format	4djo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4djo_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4djo_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4djo_validation.xml.gz	12.6 KB	Display
Data in CIF	4djo_validation.cif.gz	17.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dj/4djo ftp://data.pdbj.org/pub/pdb/validation_reports/dj/4djo	HTTPS FTP

-
Related structure data

Related structure data	4djpC 4djqC 4djrC C: citing same article (ref.)
Similar structure data	1fg6-d 4mc6-d 2i4w-d 1f7a-d 2f81-d 1mrx-d 4coe-d 2qci-d 2i4d-d 1lzq-d 5hvp-d 4mc1-d 5ivt-d 3kdb-d 1ajv-d 3qro-d 3ndu-2 1mt9-d 5ah9-d 3zpu-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#6 - Jun 2000 HIV-1 Protease similarity (1)

Deposited unit

A: Pol polyprotein

B: Pol polyprotein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.732, 57.763, 61.736
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 2 molecules AB

#1: Protein	Pol polyprotein / HIV-1 Protease Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: unp residues 1-99 / Mutation: K7Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: SF2 / Gene: gag-pol, pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: Q90K99

#1: Protein

Pol polyprotein / HIV-1 Protease

Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: unp residues 1-99 / Mutation: K7Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus 1 / Strain: SF2 / Gene: gag-pol, pol / Plasmid: pXC35 / Production host:

Escherichia coli (E. coli) / Strain (production host): TAP56 / References: UniProt: Q90K99

-
Non-polymers , 5 types, 167 molecules

#2: Chemical	ChemComp-MK5 / 2-[(dichloroacetyl)amino]ethyl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl][(2S)-2-methylbutyl]amino}-1-phenylbutan-2-yl]carbamate Mass: 618.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₇Cl₂N₃O₇S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.17 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126mM Phosphate buffer, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.78→50 Å / Num. obs: 17839 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / R_merge(I) obs: 0.043 / Χ²: 1.036 / Net I/σ(I): 16.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.78-1.84	6.6	0.227	1721	1.007	1	97.7
1.84-1.92	6.8	0.164	1749	1.055	1	97.8
1.92-2	6.8	0.128	1737	1.069	1	98
2-2.11	6.8	0.101	1744	0.994	1	98.6
2.11-2.24	6.9	0.083	1763	1.027	1	98.5
2.24-2.42	6.8	0.072	1770	0.972	1	99
2.42-2.66	6.9	0.056	1794	1.069	1	99.4
2.66-3.04	6.9	0.041	1804	0.94	1	99.6
3.04-3.83	6.9	0.028	1833	1.078	1	99.8
3.83-50	6.6	0.023	1924	1.139	1	98.8

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.78→39.2 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.2203 / WR_factor R_work: 0.1617 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8691 / SU B: 5.602 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1338 / SU R_free: 0.1335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2166	904	5.1 %	RANDOM
R_work	0.1597	-	-	-
obs	0.1626	17747	98.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 57.47 Å² / B_iso mean: 28.6079 Å² / B_iso min: 17.84 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.48 Å²	0 Å²	0 Å²
2-	-	0.08 Å²	0 Å²
3-	-	-	0.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→39.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1514	0	60	162	1736

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1812
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1255
X-RAY DIFFRACTION	r_angle_refined_deg	1.31	2.059	2474
X-RAY DIFFRACTION	r_angle_other_deg	0.792	3.011	2980
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.838	5	222
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.679	24.194	62
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.287	15	309
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.13	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	283
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	1963
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	314
X-RAY DIFFRACTION	r_mcbond_it	0.541	1.5	1059
X-RAY DIFFRACTION	r_mcbond_other	0.175	1.5	438
X-RAY DIFFRACTION	r_mcangle_it	0.941	2	1742
X-RAY DIFFRACTION	r_scbond_it	1.617	3	753
X-RAY DIFFRACTION	r_scangle_it	2.559	4.5	732

LS refinement shell

Resolution: 1.777→1.823 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.253	59	-
R_work	0.176	1208	-
all	-	1267	-
obs	-	-	95.84 %

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	1.102	-1.7845	-1.1824	3.1879	1.0722	3.9562	-0.0718	0.0143	-0.1268	0.1322	-0.0213	0.1831	0.173	-0.096	0.0931	0.0867	-0.0187	-0.0049	0.0724	0.009	0.0995	20.2439	14.0726	22.4532
2	9.4593	-0.1509	-1.9409	1.8979	-0.0039	2.2136	-0.0243	0.0963	-0.0799	-0.052	0.0311	0.1849	-0.0084	-0.1713	-0.0069	0.0623	-0.0135	-0.0107	0.0494	0.0098	0.08	10.977	19.2587	17.7265
3	3.93	-1.0336	-0.5537	2.717	-0.0827	0.1035	0.1955	0.1379	0.1032	-0.1112	-0.1541	0.4274	-0.0382	-0.0296	-0.0414	0.1389	0.0336	-0.0401	0.2376	-0.0085	0.251	-0.1799	23.064	16.2635
4	5.5668	1.4062	3.8944	0.9124	1.2278	5.646	0.1758	-0.0267	-0.2741	0.0274	-0.0352	0.1074	0.3009	-0.2436	-0.1407	0.0923	0.0004	-0.0218	0.0652	0.001	0.0958	14.026	23.2245	18.8862
5	7.7318	-1.1439	2.5951	1.0403	-0.817	2.4348	0.0357	-0.0577	0.0766	-0.0442	-0.0001	0.1061	-0.0342	-0.1437	-0.0356	0.0773	0.0096	-0.003	0.0513	-0.0001	0.052	12.6164	32.2236	19.079
6	11.7688	-2.7767	-2.3104	6.3562	1.7371	7.9461	0.0092	0.3339	-0.2684	-0.1805	0.0142	0.0867	0.3021	-0.4247	-0.0234	0.1148	-0.0166	-0.0109	0.1229	0.0214	0.0921	2.7689	29.8615	9.9119
7	7.0783	0.5775	1.7204	1.6368	-1.43	2.2264	-0.0738	0.001	0.2748	-0.0933	0.0904	0.2305	0.0577	-0.2992	-0.0166	0.113	0.0099	0.0189	0.2343	-0.0174	0.191	-1.4066	38.8691	15.9416
8	14.3582	-7.6321	-3.7793	7.9445	-0.2426	2.3338	0.0153	0.1126	-0.0967	0.0924	0.0377	0.2289	-0.0415	-0.0233	-0.0529	0.0869	-0.0038	0.0018	0.1064	-0.0058	0.0609	12.4631	40.825	13.5379
9	3.7813	-0.2543	0.0853	2.8493	-0.4041	1.0478	0.1655	0.0853	0.0761	-0.1309	-0.1474	-0.1411	0.1793	0.0657	-0.0181	0.082	0.0102	0.0066	0.0894	0.0053	0.059	15.997	37.7809	9.615
10	3.6093	1.7872	-3.804	6.5687	-3.0628	4.6924	0.1489	0.0136	0.1064	0.2021	0.153	0.1135	-0.1675	-0.141	-0.3019	0.0368	0.0163	-0.005	0.1012	0.0253	0.1138	1.5268	36.0054	20.1059
11	5.9828	-1.7251	5.7856	4.7725	-0.5609	5.8837	0.2239	0.0349	-0.1892	0.0889	-0.0797	0.1179	0.2538	0.0051	-0.1442	0.1472	0.0352	0.0471	0.1432	0.0094	0.1485	4.7889	21.2506	26.0296
12	1.0311	0.6603	-1.7371	6.7546	-1.6397	2.9797	-0.0422	0.0097	0.0078	0.0829	0.0511	0.1335	0.0528	-0.0443	-0.0089	0.0666	0.0115	-0.0099	0.102	0.0129	0.0953	3.37	30.1751	25.824
13	2.1066	-2.0441	-0.4481	2.9391	0.5627	5.0088	0.039	0.2731	0.0908	-0.1236	-0.0066	0.0513	0.2366	0.0815	-0.0324	0.0872	-0.0033	-0.0086	0.1152	0.0251	0.1022	9.0654	32.3782	10.8652
14	2.8376	-0.0417	2.4415	2.1218	0.5972	4.1096	-0.007	-0.0345	-0.0601	-0.1046	0.0434	0.2153	0.0009	-0.0119	-0.0364	0.0755	0.0029	-0.0061	0.0473	0.0165	0.0567	12.7789	28.0272	18.7718
15	4.0105	-2.3435	-1.4888	4.4135	-0.5372	1.2038	-0.2241	-0.1799	-0.13	0.1292	0.2709	0.2444	0.0707	-0.0247	-0.0468	0.1136	0.0271	0.021	0.171	0.0367	0.0948	10.622	29.0574	27.9049
16	8.6301	-3.3961	-0.4364	4.1078	-0.3193	2.5194	-0.185	-0.1143	0.0377	0.2846	0.1756	-0.0238	-0.0768	-0.0319	0.0094	0.0861	0.0226	0.0201	0.0746	0.0086	0.0348	20.1899	22.0541	30.3365
17	2.0265	-0.5571	1.6139	1.9956	-1.9896	3.1465	-0.0952	-0.3252	0.1055	0.1916	0.1092	-0.0818	-0.1381	-0.098	-0.014	0.1279	0.0272	0.0004	0.1356	-0.0462	0.0664	20.6629	27.8663	32.5573
18	9.3461	-0.0079	0.0341	0.9973	-0.2615	0.1187	-0.0026	-0.0726	0.3328	0.0865	-0.0533	-0.1238	-0.0997	-0.0119	0.0559	0.1369	0.0117	-0.0309	0.0856	-0.0063	0.0728	28.7223	32.0264	25.9184
19	4.0464	2.526	-3.3687	3.0836	-1.8546	2.8475	0.0494	-0.22	0.0963	0.2545	0.137	-0.2337	-0.0554	0.2356	-0.1864	0.1736	-0.0245	-0.0217	0.1642	0.0103	0.2733	42.4556	30.8784	21.3088
20	6.0206	1.988	0.8501	4.643	-0.2332	1.0559	-0.1526	0.0815	0.2752	0.167	-0.0114	-0.1363	-0.2488	0.1047	0.164	0.098	-0.0024	-0.0294	0.0679	0.0077	0.0547	32.0998	32.2642	23.2639
21	4.6756	1.9435	1.0701	1.5188	0.093	0.4193	-0.0325	0.2728	-0.0961	-0.0937	0.0396	-0.0737	0.0319	0.0937	-0.0071	0.0815	0.0125	0.0015	0.0687	0.0015	0.049	24.5027	24.2789	15.6845
22	13.3741	1.1814	0.8337	3.6764	0.4953	2.3999	-0.0418	0.2729	0.3257	-0.0063	-0.092	-0.3878	-0.241	0.1033	0.1338	0.103	-0.0092	-0.0091	0.1061	0.0427	0.0755	34.2557	33.8985	13.0152
23	5.9202	2.3142	3.596	2.1353	3.3519	5.275	-0.0393	0.1701	-0.0332	-0.0336	0.2108	-0.1145	-0.0459	0.404	-0.1714	0.0918	-0.0032	0.0215	0.1665	0.0505	0.1207	42.7709	28.8854	7.9754
24	18.2768	-0.7243	-2.4114	1.1918	0.511	0.5886	-0.0086	0.0496	-0.9717	0.0457	-0.0701	0.103	0.1105	0.1417	0.0786	0.1717	0.0965	-0.0049	0.2239	-0.0463	0.1088	31.4232	26.4666	2.3581
25	1.3191	-0.4461	-1.9521	1.4722	-0.0994	3.5861	-0.014	0.0427	-0.0913	0.0216	0.0467	0.09	-0.1036	-0.2404	-0.0327	0.0939	0.032	0.0269	0.1515	0.0209	0.1069	21.1531	31.6931	5.9013
26	5.514	-4.0303	3.9704	4.7108	-3.6734	4.5898	0.0979	0.2309	-0.1192	0.0069	-0.1971	0.0244	-0.0167	0.3361	0.0993	0.0582	0.0128	0.0152	0.0842	0.0082	0.0395	36.5162	26.2672	7.1115
27	7.1538	-3.1231	-8.997	3.9884	4.7608	12.2718	-0.0101	-0.0887	0.2232	0.0679	0.0682	0.007	-0.0169	0.2244	-0.0581	0.0531	-0.0263	-0.0313	0.0834	0.0256	0.1217	38.5202	23.776	21.0359
28	1.1819	0.0677	-0.2778	2.3553	0.2277	4.0072	0.0197	-0.0843	0.0655	0.1763	-0.003	-0.1502	0.0014	-0.0041	-0.0167	0.0526	0.0043	0.0003	0.0618	0.008	0.094	36.2323	20.795	22.3874
29	0.4153	0.3591	-1.2084	2.8333	0.2703	4.2376	0.0203	0.0332	-0.0137	-0.097	-0.0833	0.0332	-0.2192	-0.0922	0.063	0.0721	-0.0155	-0.01	0.101	0.0237	0.0642	31.1715	32.1687	10.9215
30	2.1561	4.1297	0.0853	15.9101	-3.0297	2.7612	-0.1395	0.0882	0.1682	0.0742	0.2459	0.2419	-0.2698	0.0351	-0.1064	0.0521	-0.0102	0.0211	0.0616	0.0048	0.0792	28.3731	31.0716	17.9082
31	0.9517	-0.8955	0.2322	0.9484	-0.337	1.4451	-0.069	-0.043	-0.0501	0.022	-0.0091	-0.0349	0.045	0.0562	0.0781	0.0607	0.0088	0.0106	0.0686	0.0177	0.0827	29.271	18.7523	20.2333
32	2.6779	-1.886	-1.6476	3.0184	1.3286	3.6512	-0.1138	0.1007	-0.1102	0.1297	0.0283	0.1675	0.2748	-0.2355	0.0855	0.096	0.0104	0.0048	0.0874	0.0141	0.0487	18.6163	18.3471	28.1779

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	1 - 7
2	X-RAY DIFFRACTION	2	B	8 - 14
3	X-RAY DIFFRACTION	3	B	15 - 20
4	X-RAY DIFFRACTION	4	B	21 - 26
5	X-RAY DIFFRACTION	5	B	27 - 33
6	X-RAY DIFFRACTION	6	B	34 - 37
7	X-RAY DIFFRACTION	7	B	38 - 43
8	X-RAY DIFFRACTION	8	B	44 - 49
9	X-RAY DIFFRACTION	9	B	50 - 56
10	X-RAY DIFFRACTION	10	B	57 - 63
11	X-RAY DIFFRACTION	11	B	64 - 69
12	X-RAY DIFFRACTION	12	B	70 - 75
13	X-RAY DIFFRACTION	13	B	76 - 81
14	X-RAY DIFFRACTION	14	B	82 - 87
15	X-RAY DIFFRACTION	15	B	88 - 92
16	X-RAY DIFFRACTION	16	B	93 - 99
17	X-RAY DIFFRACTION	17	A	1 - 7
18	X-RAY DIFFRACTION	18	A	8 - 13
19	X-RAY DIFFRACTION	19	A	14 - 18
20	X-RAY DIFFRACTION	20	A	19 - 24
21	X-RAY DIFFRACTION	21	A	25 - 31
22	X-RAY DIFFRACTION	22	A	32 - 36
23	X-RAY DIFFRACTION	23	A	37 - 42
24	X-RAY DIFFRACTION	24	A	43 - 47
25	X-RAY DIFFRACTION	25	A	48 - 54
26	X-RAY DIFFRACTION	26	A	55 - 61
27	X-RAY DIFFRACTION	27	A	62 - 66
28	X-RAY DIFFRACTION	28	A	67 - 74
29	X-RAY DIFFRACTION	29	A	75 - 81
30	X-RAY DIFFRACTION	30	A	82 - 86
31	X-RAY DIFFRACTION	31	A	87 - 94
32	X-RAY DIFFRACTION	32	A	95 - 99

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 167 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 167 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 167 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi