PDB-2fns: Crystal structure of wild-type inactive (D25N) HIV-1 protease com...

ID or keywords:

Entry

Database: PDB / ID: 2fns

Title

Crystal structure of wild-type inactive (D25N) HIV-1 protease complexed with wild-type HIV-1 NC-p1 substrate.

Components

NC-P1 SUBSTRATE PEPTIDE
Protease

Keywords

HYDROLASE / structural intermediate / substrate recognition /

hiv-1 protease / NC-p1 substrate /

drug resistance / flap conformation

Function / homology

Function and homology information

RNA stem-loop binding /

host cell /

HIV-1 retropepsin /

retroviral ribonuclease H /

exoribonuclease H /

exoribonuclease H activity / host multivesicular body / DNA integration /

RNA-directed DNA polymerase / viral genome integration into host DNA ...
Similarity search - Function

Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain /

Integrase, C-terminal domain superfamily, retroviral /

Integrase, N-terminal zinc-binding domain ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus 1

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Prabu-Jeyabalan, M. / Nalivaika, E.A. / Schiffer, C.A.

Citation

Journal: J.Virol. / Year: 2006
Title: Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate.
Authors: Prabu-Jeyabalan, M. / Nalivaika, E.A. / Romano, K. / Schiffer, C.A.

History

Deposition	Jan 11, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 5, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 20, 2021	Group: Database references / Derived calculations / Category: 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
Revision 1.5	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2fns.cif.gz	56.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2fns.ent.gz	42.9 KB	Display	PDB format
PDBx/mmJSON format	2fns.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fn/2fns ftp://data.pdbj.org/pub/pdb/validation_reports/fn/2fns	HTTPS FTP

-
Related structure data

Related structure data	2fntC 1t3rS 1tsu C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1f7a-d 3hbo-d 3s43-d 5kr1-d 2qnq-d 4q1x-d 5ah9-d 3oxv-2 3tlh-1 2q54-d 6mcr-1 1kjg-d 3em3-d 2i4d-d 3nu6-d 1qbt-d 3zpu-d 3cyx-d 3qaa-d 4q1w-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 (2) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Protease

B: Protease

P: NC-P1 SUBSTRATE PEPTIDE

hetero molecules

23 kDa, 3 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)	51.060, 57.369, 61.302
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Protease / / Retropepsin / PR Mass: 10800.777 Da / Num. of mol.: 2 / Mutation: Q7K, D25N, L63P, I64V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: HXB2 / Gene: GAG / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 References: UniProt: O38716, UniProt: P03369*PLUS, HIV-1 retropepsin
#2: Protein/peptide	NC-P1 SUBSTRATE PEPTIDE Mass: 1162.342 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence of this peptide occurs naturally in Human immunodeficiency virus (HIV)
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 109 / 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: 1.97 Å³/Da / Density % sol: 37.59 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126mM Sodium phosphate pH 6.2; 63mM sodium citrate; ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 15, 2002 / Details: Osmic Mirrors
Radiation	Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.85→42 Å / Num. all: 14812 / Num. obs: 14812 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / R_merge(I) obs: 0.056 / R_sym value: 0.056 / Net I/σ(I): 8.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T3R

1t3r

Resolution: 1.85→23 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.929 / SU B: 8.315 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.196 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24308	1503	10.2 %	RANDOM
R_work	0.19474	-	-	-
all	0.19968	14812	-	-
obs	0.19968	13281	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 27.948 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.28 Å²	0 Å²	0 Å²
2-	-	0.28 Å²	0 Å²
3-	-	-	1 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1612	0	17	110	1739

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	1663
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	1629
X-RAY DIFFRACTION	r_angle_refined_deg	1.034	1.985	2277
X-RAY DIFFRACTION	r_angle_other_deg	0.624	3	3781
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.733	5	222
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.862	24.821	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.913	15	279
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.145	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	272
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1869
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	299
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.3	267
X-RAY DIFFRACTION	r_nbd_other	0.2	0.3	1638
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.5	766
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.5	965
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.201	0.5	157
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.039	0.5	2
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.118	0.3	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.199	0.3	77
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.12	0.5	15
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.725	1.5	1398
X-RAY DIFFRACTION	r_mcbond_other	0.125	1.5	449
X-RAY DIFFRACTION	r_mcangle_it	0.749	2	1754
X-RAY DIFFRACTION	r_scbond_it	1.395	3	656
X-RAY DIFFRACTION	r_scangle_it	1.861	4.5	523
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	63	-
R_work	0.323	598	-
obs	-	-	100 %

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	3.8061	-2.2452	-0.9657	4.0971	1.5674	4.3399	-0.1309	0.0703	-0.3715	0.1322	-0.0299	0.3925	0.3895	0.0732	0.1608	-0.0412	0.0039	0.041	-0.0781	0.0355	-0.0528	19.7276	17.908	22.9659
2	3.8812	0.5792	-1.3614	4.0602	0.64	3.5471	-0.0331	-0.2914	0.216	0.3736	0.0758	0.1257	-0.0634	0.1543	-0.0427	-0.0256	0.023	0.024	-0.006	-0.0002	-0.127	20.7836	26.2692	28.8155
3	47.5801	-5.3795	3.3009	1.172	1.3814	5.6898	0.249	0.9061	-2.4342	-0.2696	-0.1908	0.4012	0.1065	-0.203	-0.0582	0.0007	-0.0486	0.0364	0.0603	0.0136	0.3067	1.9571	21.4699	16.4981
4	10.6522	-4.3072	2.591	5.829	-1.4579	1.9097	-0.0717	0.3479	-0.4076	-0.2173	0.0327	0.4553	0.0059	-0.0297	0.039	-0.0736	-0.0179	0.0315	-0.0853	0.0062	-0.0808	14.0251	27.433	18.2729
5	7.818	-6.7291	-6.9409	11.8319	5.502	9.4557	0.0701	1.0384	-0.0424	-0.1988	0.1104	0.6706	0.307	-1.152	-0.1805	-0.0399	0.0041	-0.0298	0.0933	0.0944	0.1294	0.8832	34.0491	12.9851
6	24.6336	-5.316	-8.7925	7.3091	3.9096	10.317	0.3225	0.254	0.1311	-0.0743	-0.1002	-0.7363	-0.1283	0.25	-0.2223	-0.0471	-0.0153	-0.0514	-0.0758	0.0324	-0.0672	38.2636	30.9901	23.9257
7	5.6138	1.7219	-0.7849	2.9645	0.6897	1.8789	-0.0514	0.0998	0.2201	-0.0947	-0.1127	0.1436	-0.1888	-0.0847	0.1642	-0.0614	0.0183	-0.0063	-0.0834	0.0318	-0.1184	26.733	27.5791	18.5895
8	4.5503	2.9636	3.4726	18.1281	4.8733	3.9909	0.3737	-0.1495	0.0102	-0.2463	-0.1512	-2.2658	-0.1444	0.9805	-0.2225	-0.0231	0.0285	0.0802	0.1507	0.1754	0.1359	40.0385	30.8402	11.2173
9	18.0839	-6.2844	0.4859	7.326	-2.0947	7.1136	0.1805	0.0403	-0.4313	0.0013	0.0194	0.3626	0.0783	0.1894	-0.1999	-0.0684	-0.0171	-0.0207	-0.1419	-0.0124	-0.1129	14.5535	38.8007	10.8587
10	26.8545	-4.2775	4.6794	3.9293	-1.1701	7.9889	0.2653	0.5825	-0.192	-1.2575	-0.53	1.0343	0.5126	-0.1453	0.2647	0.1635	0.0415	-0.1278	-0.0273	-0.0969	0.054	27.1924	30.5286	3.3282
11	8.7303	1.8409	-3.5287	15.8308	-11.3555	8.7179	0.2271	-0.0471	0.6762	0.6593	0.7616	1.0654	-0.2956	-0.4262	-0.9887	-0.0666	0.0249	0.0665	-0.0298	0.0536	0.0751	1.7359	36.4899	18.4119
12	3.5175	-5.4517	0.762	32.419	-9.8466	7.8724	-0.5146	0.0687	-0.2662	0.0952	0.616	0.6548	0.3768	-0.1941	-0.1014	-0.0485	0.0114	0.0308	-0.0529	0.0711	0.0675	3.4122	22.9856	23.3742
13	3.6982	0.5732	-2.9183	10.1472	-6.4028	6.3437	0.0097	-0.5175	-0.2111	0.5061	-0.301	0.124	-0.2749	0.3	0.2914	-0.0688	0.0333	0.0418	-0.064	0.0484	0.0234	4.511	29.8981	23.2787
14	10.6413	-7.47	4.7625	8.1618	-10.0494	17.5437	0.1635	0.4553	0.2675	-0.1876	-0.6246	-0.6907	-0.0878	0.7225	0.4612	-0.0934	0.0103	0.0791	-0.032	0.0557	-0.0008	39.2695	25.0559	10.1278
15	16.2101	2.123	-18.9572	3.9102	-2.9207	36.5866	-0.0922	-0.5649	0.3351	0.8464	0.1971	-0.7186	0.3336	0.6527	-0.1049	-0.0043	0.0343	-0.0981	-0.1115	0.0017	-0.0354	37.0891	24.0147	24.5197
16	3.8473	-3.5707	1.5401	7.1215	-2.003	0.7029	0.0086	0.027	0.1808	0.1365	-0.1463	-0.483	-0.1455	0.1585	0.1377	-0.0776	0.0212	0.0147	-0.0721	-0.0045	-0.1129	36.0905	21.7541	17.9232
17	1.2172	-2.3645	2.0057	7.2025	-5.9098	7.1096	0.3811	0.3359	-0.3226	-0.9418	-0.0657	0.5552	0.6208	0.5039	-0.3155	-0.042	0.0146	-0.0402	-0.0084	0.0134	-0.0592	10.9211	28.932	11.7897
18	2.2033	2.6348	-6.1505	10.2747	-8.2536	17.2827	0.3755	0.3164	0.5707	0.2806	0.3648	0.7045	-0.7834	-0.3263	-0.7403	-0.0981	-0.0114	-0.0065	-0.0374	0.0792	-0.0709	29.6666	32.9021	14.9441
19	6.7607	-0.4776	0.3468	2.4953	1.6435	4.6193	-0.1294	-0.2455	0.0706	0.1722	0.3292	0.2406	-0.0282	-0.1591	-0.1998	-0.0986	0.0299	0.0668	-0.0929	0.0301	-0.0688	11.5697	28.6372	26.1078
20	6.1442	-3.8984	1.8382	4.9222	-0.2709	2.6623	0.0344	0.0714	-0.4332	0.0311	-0.0501	0.0097	0.0452	0.0035	0.0157	-0.0766	-0.0247	-0.0167	-0.0973	0.0054	-0.1432	29.0469	19.571	19.7607
21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 5	1 - 5
2	X-RAY DIFFRACTION	1	A	A	94 - 99	94 - 99
3	X-RAY DIFFRACTION	1	A	A	6 - 10	6 - 10
4	X-RAY DIFFRACTION	2	B	B	1 - 5	1 - 5
5	X-RAY DIFFRACTION	2	B	B	94 - 99	94 - 99
6	X-RAY DIFFRACTION	2	B	B	6 - 10	6 - 10
7	X-RAY DIFFRACTION	3	A	A	11 - 20	11 - 20
8	X-RAY DIFFRACTION	4	A	A	21 - 32	21 - 32
9	X-RAY DIFFRACTION	5	A	A	33 - 43	33 - 43
10	X-RAY DIFFRACTION	6	B	B	11 - 20	11 - 20
11	X-RAY DIFFRACTION	7	B	B	21 - 32	21 - 32
12	X-RAY DIFFRACTION	8	B	B	33 - 43	33 - 43
13	X-RAY DIFFRACTION	9	A	A	44 - 56	44 - 56
14	X-RAY DIFFRACTION	10	B	B	44 - 56	44 - 56
15	X-RAY DIFFRACTION	11	A	A	57 - 62	57 - 62
16	X-RAY DIFFRACTION	12	A	A	63 - 68	63 - 68
17	X-RAY DIFFRACTION	13	A	A	69 - 76	69 - 76
18	X-RAY DIFFRACTION	14	B	B	57 - 62	57 - 62
19	X-RAY DIFFRACTION	15	B	B	63 - 68	63 - 68
20	X-RAY DIFFRACTION	16	B	B	69 - 76	69 - 76
21	X-RAY DIFFRACTION	17	A	A	77 - 85	77 - 85
22	X-RAY DIFFRACTION	18	B	B	77 - 85	77 - 85
23	X-RAY DIFFRACTION	19	A	A	86 - 93	86 - 93
24	X-RAY DIFFRACTION	20	B	B	86 - 93	86 - 93
25	X-RAY DIFFRACTION	21	P	C	2 - 8	1 - 7

-
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://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

-
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

-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

-
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