PDB-2nxd: Structure of HIV-1 protease D25N complexed with rt-rh analogue pe...

ID or keywords:

Entry

Database: PDB / ID: 2nxd

Title

Structure of HIV-1 protease D25N complexed with rt-rh analogue peptide GLY-ALA-ASP-ILE-PHE*TYR-LEU-ASP-GLY-ALA

Components

Analogue of RT-RH pol protease substrate peptide
PROTEASE RETROPEPSIN

Keywords

HYDROLASE/HYDROLASE SUBSTRATE / peptide design / molecular dynamics / hiv protease / substrate recognition / calorimetry / HYDROLASE-HYDROLASE SUBSTRATE COMPLEX

Function / homology

Function and homology information

HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...
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

HIV-1 M:B_ARV2/SF2 (virus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

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

Citation

Journal: Proteins / Year: 2007
Title: Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease
Authors: Altman, M.D. / Nalivaika, E.A. / Prabu-Jeyabalan, M. / Schiffer, C.A. / Tidor, B.

History

Deposition	Nov 17, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 18, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 18, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3	Oct 20, 2021	Group: Advisory / Database references Category: database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2nxd.cif.gz	54.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2nxd.ent.gz	40.6 KB	Display	PDB format
PDBx/mmJSON format	2nxd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2nxd_validation.pdf.gz	373.9 KB	Display	wwPDB validaton report
Full document	2nxd_full_validation.pdf.gz	376.3 KB	Display
Data in XML	2nxd_validation.xml.gz	5.4 KB	Display
Data in CIF	2nxd_validation.cif.gz	8.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/2nxd ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nxd	HTTPS FTP

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Related structure data

Related structure data	2nxlC 2nxmC 1t3rS 1kjg C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4hvp-d 2nxl-d 3bgb-d 3gga-1 6opy-d 3cyw-d 3o9h-d 1hos-d 1yth-d 4m8x-d 3bgc-d 1mtb-d 5ah6-d 4q1x-d 1izi-d 6pji-d 1ec1-d 6oy1-d 5kr2-3 6kmp-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	#6 - Jun 2000 HIV-1 Protease similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: PROTEASE RETROPEPSIN

B: PROTEASE RETROPEPSIN

P: Analogue of RT-RH pol protease substrate peptide

22.7 kDa, 3 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)	51.171, 57.692, 61.482
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 / E.C.3.4.23.16 / HIV-1 PROTEASE Mass: 10814.805 Da / Num. of mol.: 2 / Mutation: Q7K, D25N, L63P Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: SF2 / Gene: pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap106 References: UniProt: O38732, UniProt: P03369*PLUS, HIV-1 retropepsin
#2: Protein/peptide	Analogue of RT-RH pol protease substrate peptide Mass: 1041.113 Da / Num. of mol.: 1 / Fragment: decapeptide fragment / Mutation: EP3D/TP2I//VP2'L / Source method: obtained synthetically Details: This sequence was custom-designed and then purchased commercially
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H₂O

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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 Å³/Da / Density % sol: 38.51 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126 mM sodium phosphate pH 6.2; 63mM sodium citrate; 25-35%Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Mar 29, 2005 / Details: Yale Mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→42.07 Å / Num. all: 11909 / Num. obs: 11909 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / R_merge(I) obs: 0.034 / R_sym value: 0.034 / Net I/σ(I): 21.2

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Processing

Software

Name	Version	Classification
AMoRE		phasing
REFMAC	5.2	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1T3R - Crystal structure of HIV-1 protease complexed with the inhibitor TMC114

1t3r

Resolution: 2→42.07 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.914 / SU B: 9.509 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25737	586	4.9 %	RANDOM
R_work	0.19505	-	-	-
all	0.1979	11295	-	-
obs	0.1979	11295	92.82 %	-

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: 46.962 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.82 Å²	0 Å²	0 Å²
2-	-	-0.8 Å²	0 Å²
3-	-	-	1.62 Å²

Refinement step

Cycle: LAST / Resolution: 2→42.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1540	0	0	74	1614

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	1570
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	1541
X-RAY DIFFRACTION	r_angle_refined_deg	1.218	1.98	2144
X-RAY DIFFRACTION	r_angle_other_deg	0.678	3	3566
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.125	5	209
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.513	24.706	51
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.756	15	250
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.62	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	259
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1746
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	281
X-RAY DIFFRACTION	r_nbd_refined	0.188	0.2	245
X-RAY DIFFRACTION	r_nbd_other	0.19	0.2	1499
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	736
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	1025
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	70
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.15	0.2	8
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.198	0.2	43
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.144	0.2	7
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	0.786	1.5	1331
X-RAY DIFFRACTION	r_mcbond_other	0.163	1.5	441
X-RAY DIFFRACTION	r_mcangle_it	0.986	2	1665
X-RAY DIFFRACTION	r_scbond_it	1.514	3	604
X-RAY DIFFRACTION	r_scangle_it	2.177	4.5	479
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.271	45	-
R_work	0.218	885	-
obs	-	-	99.15 %

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	4.2037	2.3135	4.0763	4.6507	0.8298	6.8287	-0.1187	0.3276	0.1011	-0.5317	0.1003	0.2297	-0.157	0.1002	0.0183	-0.1628	-0.0115	-0.0666	-0.1849	0.0268	-0.1921	20.3764	8.4416	2.444
2	44.1391	-4.8965	15.654	7.3816	4.97	20.7887	0.7474	0.2282	-1.4019	0.0484	0.1188	0.5848	0.9755	0.1256	-0.8662	-0.081	-0.0436	-0.0448	-0.2097	-0.0562	-0.0999	20.9847	-4.5775	3.3199
3	56.2342	-9.6351	37.0252	19.3474	5.108	31.7885	-0.0567	2.0808	0.4945	-0.4644	0.1248	-1.1792	-0.3878	1.5853	-0.0681	-0.0569	-0.0434	0.0686	-0.069	0.0881	0.0814	40.865	-1.3251	7.9803
4	28.4208	9.4208	6.2533	19.9433	-2.0543	2.3885	0.6498	-1.2217	0.7712	0.9192	-0.5838	1.3915	-0.255	-0.0834	-0.066	-0.1447	-0.006	0.0337	-0.2122	-0.1061	-0.0882	19.3479	12.5545	14.9824
5	30.9481	-2.8465	-28.0313	20.545	-16.1016	42.5927	0.0768	-1.5303	3.8464	-0.9735	0.0198	1.3968	0.9491	-0.0873	-0.0966	-0.2197	0.0848	-0.0881	-0.0756	-0.0449	0.2586	0.4287	6.0821	13.5166
6	8.4309	-3.0216	-0.5241	6.0093	-0.6537	0.1763	-0.0441	-0.0071	0.0396	0.1394	-0.0586	0.2193	0.143	-0.0952	0.1027	-0.1645	0.0029	0.0114	-0.1426	0.0476	-0.1914	27.5948	0.9129	12.5236
7	7.7515	-1.95	1.3477	13.4016	10.5678	9.4481	0.0552	0.2252	0.3838	0.4089	0.344	-1.131	0.4169	1.169	-0.3992	-0.0715	-0.0201	-0.0699	-0.0325	0.1048	0.0616	42.0116	-1.6072	20.855
8	11.1062	4.435	-4.0107	3.2188	-1.0836	3.991	0.1369	-0.0598	0.4224	-0.0135	0.0318	0.4174	-0.0254	0.1649	-0.1687	-0.1256	-0.0016	-0.0482	-0.1857	-0.0027	-0.0231	12.9967	1.5396	12.9247
9	15.7161	2.9709	-5.1024	9.6778	-2.2266	2.3536	0.2867	-0.3047	0.5015	0.5188	0.2482	1.2315	-0.5748	-0.5094	-0.535	0.011	-0.0054	0.0449	-0.1445	0.0373	-0.0171	26.6146	-1.6326	25.9955
10	6.3019	1.5064	7.0493	6.772	2.1772	19.3236	-0.5716	-0.5552	-0.5828	-0.5164	0.9687	1.1827	-0.9385	0.0828	-0.3971	-0.3018	0.0114	0.0289	0.0565	0.1501	0.1362	-1.2367	-5.6772	17.9148
11	20.6199	6.926	2.6332	12.6358	-2.0804	6.6431	0.4078	-0.4101	0.1662	0.3518	-0.1381	0.6453	-0.3708	0.1896	-0.2697	-0.1369	-0.0068	0.0048	-0.2136	0.0044	-0.1436	14.2333	-10.2784	20.0287
12	8.5773	7.4037	-9.1932	11.5458	-18.3791	31.0117	0.2371	-0.68	-0.1937	0.159	-0.5132	-0.8321	0.3822	0.5461	0.2761	-0.277	-0.005	-0.1223	-0.1082	0.074	-0.0853	39.2382	4.0091	20.8717
13	34.2335	10.8177	24.8227	17.3874	0.2629	24.1486	0.3721	-0.0829	-1.4593	-0.2083	0.3822	-0.7502	-0.1631	-0.5234	-0.7543	-0.2709	0.0266	0.0567	-0.3022	-0.0227	-0.1708	37.2671	4.5931	6.6883
14	6.3335	1.5399	0.5888	4.3842	0.8982	6.1449	-0.1211	-0.0011	0.0332	-0.0712	-0.1517	-0.5225	-0.1339	0.2195	0.2728	-0.2683	0.015	-0.0043	-0.2459	-0.0187	-0.1993	36.6231	7.2775	12.2046
15	5.124	3.4903	-1.1108	20.4167	-13.3225	8.9939	0.5662	-0.1214	-0.7762	-0.0408	1.2614	1.2405	0.0286	-0.1814	-1.8276	-0.2487	0.0169	-0.0599	-0.1871	0.0205	0.197	1.8644	-7.6813	13.3688
16	7.9529	7.926	-13.8881	59.1349	-11.861	24.3292	-0.5377	-1.2514	0.5718	-1.3399	0.5954	2.3606	-0.0758	0.1453	-0.0576	-0.2003	-0.0711	-0.1894	-0.0039	0.2583	0.3269	3.3485	5.8419	7.3387
17	5.9021	7.1147	-2.4039	8.6747	-2.351	4.0241	-0.344	0.4496	0.655	-0.3233	0.5112	1.0327	-0.0202	-0.5522	-0.1672	-0.2298	-0.0295	-0.1058	-0.1288	0.0657	0.1771	4.0961	-0.6237	6.8422
18	1.4053	-2.1076	-0.1269	8.9238	-1.4062	14.2082	-0.0497	-0.2445	-0.476	0.1987	0.0772	0.5264	0.7354	-0.2569	-0.0275	-0.1063	-0.0166	0.014	-0.2086	0.0443	-0.1346	29.7921	-3.9926	16.122
19	2.5113	4.9993	-5.7763	11.5351	-10.7799	13.6124	0.4673	-0.5313	0.5107	1.0199	-0.1845	1.1484	-0.9133	0.8205	-0.2828	-0.1493	-0.0289	0.0603	-0.1146	0.01	0.0032	10.7753	-0.1076	18.9498
20	3.651	-0.4214	1.427	6.6345	-0.5493	7.9308	-0.0988	-0.0885	0.1914	-0.0004	-0.1332	-0.0959	0.1035	-0.0513	0.232	-0.173	-0.0074	-0.0061	-0.23	-0.0102	-0.1345	29.0624	9.2291	10.9881
21	3.0019	-0.2012	1.2645	1.6583	-3.3585	9.4875	-0.1398	0.2814	-0.3783	-0.4007	0.4826	0.566	0.0059	-0.1523	-0.3428	-0.201	-0.0454	-0.0863	-0.1729	-0.0058	-0.0339	11.644	0.1014	4.6037

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	B	B	1 - 5	1 - 5
4	X-RAY DIFFRACTION	1	B	B	94 - 99	94 - 99
5	X-RAY DIFFRACTION	2	A	A	6 - 10	6 - 10
6	X-RAY DIFFRACTION	3	A	A	13 - 18	13 - 18
7	X-RAY DIFFRACTION	4	B	B	6 - 10	6 - 10
8	X-RAY DIFFRACTION	5	B	B	13 - 18	13 - 18
9	X-RAY DIFFRACTION	6	A	A	21 - 33	21 - 33
10	X-RAY DIFFRACTION	7	A	A	35 - 42	35 - 42
11	X-RAY DIFFRACTION	8	B	B	21 - 33	21 - 33
12	X-RAY DIFFRACTION	9	A	A	44 - 56	44 - 56
13	X-RAY DIFFRACTION	10	B	B	35 - 42	35 - 42
14	X-RAY DIFFRACTION	11	B	B	44 - 56	44 - 56
15	X-RAY DIFFRACTION	12	A	A	57 - 62	57 - 62
16	X-RAY DIFFRACTION	13	A	A	63 - 68	63 - 68
17	X-RAY DIFFRACTION	14	A	A	69 - 76	69 - 76
18	X-RAY DIFFRACTION	15	B	B	57 - 62	57 - 62
19	X-RAY DIFFRACTION	16	B	B	63 - 68	63 - 68
20	X-RAY DIFFRACTION	17	B	B	69 - 76	69 - 76
21	X-RAY DIFFRACTION	18	A	A	77 - 85	77 - 85
22	X-RAY DIFFRACTION	19	B	B	77 - 85	77 - 85
23	X-RAY DIFFRACTION	20	A	A	86 - 93	86 - 93
24	X-RAY DIFFRACTION	21	B	B	86 - 93	86 - 93

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