PDB-2nxm: Structure of HIV-1 protease D25N complexed with the rt-rh analogu...

ID or keywords:

Entry

Database: PDB / ID: 2nxm

Title

Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide GLY-ALA-GLN-THR-PHE*TYR-VAL-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 / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...
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: 2.25 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: Refinement description / Category: software
Revision 1.3	Oct 20, 2021	Group: Database references / Category: database_2 / 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	2nxm.cif.gz	54.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2nxm.ent.gz	40.1 KB	Display	PDB format
PDBx/mmJSON format	2nxm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2nxm_validation.pdf.gz	371.4 KB	Display	wwPDB validaton report
Full document	2nxm_full_validation.pdf.gz	372.8 KB	Display
Data in XML	2nxm_validation.xml.gz	5.5 KB	Display
Data in CIF	2nxm_validation.cif.gz	8.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/2nxm ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nxm	HTTPS FTP

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Related structure data

Related structure data	2nxdC 2nxlC 1t3rS 1kjg C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1ff0-d 2nxl-d 1daz-d 3bgb-d 3zpt-d 1wbm-d 1mtb-d 1ec3-d 2fgu-d 2nxd-d 4obh-2 6opu-d 4cps-d 6pjf-d 4hvp-d 4qj7-2 3ekq-d 1fej-d 6ogq-1 6pji-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)	51.074, 58.535, 61.711
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: 1028.073 Da / Num. of mol.: 1 / Fragment: decapeptide fragment / Mutation: EP3Q / 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.: 71 / 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: 2.03 Å³/Da / Density % sol: 39.54 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 126mM sodium phosphate pH 6.2; 63mM sodium citrate; 25-35% Ammonium sulphate, 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 31, 2005 / Details: Yale
Radiation	Monochromator: Yale / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.25→42.49 Å / Num. all: 8523 / Num. obs: 8523 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.065 / R_sym value: 0.065 / Net I/σ(I): 10.3

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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 bound with TMC114

1t3r

Resolution: 2.25→42.49 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.922 / SU B: 11.86 / SU ML: 0.186 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.444 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24386	405	4.8 %	RANDOM
R_work	0.18702	-	-	-
all	0.18977	8037	-	-
obs	0.18977	8037	91.66 %	-

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: 59.773 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.47 Å²	0 Å²	0 Å²
2-	-	1.91 Å²	0 Å²
3-	-	-	0.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→42.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1542	0	0	71	1613

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	1571
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.264	1.974	2142
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.224	5	203
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.553	24.828	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.778	15	253
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.234	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	256
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1163
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	640
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	1071
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	85
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	0.171	0.2	38
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.202	0.2	4
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	0.946	1.5	1040
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.378	2	1640
X-RAY DIFFRACTION	r_scbond_it	2.147	3	597
X-RAY DIFFRACTION	r_scangle_it	3.141	4.5	502
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.269	20	-
R_work	0.289	389	-
obs	-	-	61.5 %

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	3.3038	-1.9254	1.8571	1.1316	-0.9596	2.6312	-0.3359	-0.2861	0.1127	0.0557	0.2569	-0.0177	-0.2066	-0.0652	0.079	0.0637	0.0397	-0.0224	-0.0228	-0.0081	-0.0512	4.838	8.9278	28.8866
2	10.9108	-3.3543	-3.3722	3.3386	-2.2507	5.726	-0.2076	-0.7	-0.5347	0.2937	-0.0066	0.1775	-0.0766	-0.5067	0.2142	0.0418	0.0503	0.0008	-0.0423	-0.0172	-0.0289	4.1418	-3.9031	28.36
3	7.8682	0.6728	-1.2446	0.1106	-0.4927	3.0111	0.0435	0.0674	0.6545	-0.1818	0.1148	-0.3979	-0.2426	0.2595	-0.1583	0.046	-0.011	-0.0297	-0.0901	-0.0215	0.0261	5.8912	12.7228	16.6592
4	4.8481	0.9583	-0.9295	1.0788	-0.2177	0.1795	-0.0089	0.2321	0.0709	0.0191	-0.1058	-0.03	-0.0133	0.0812	0.1147	0.0245	-0.0106	0.0101	-0.0006	-0.0055	-0.0189	-0.1364	3.1243	16.9839
5	4.7477	-0.0011	-1.1723	1.5018	-0.2177	3.3214	-0.192	0.1299	-0.1992	0.0408	0.2168	0.258	-0.0022	0.0869	-0.0248	-0.0017	-0.0152	-0.0196	-0.0365	-0.0049	-0.0127	10.3139	-0.3507	19.81
6	11.028	-0.7613	-0.3041	3.1524	0.0922	0.01	0.0558	0.5638	-0.1663	-0.4802	-0.1005	-0.2966	0.0475	0.2052	0.0447	0.0505	0.0045	0.0128	-0.0265	-0.0047	-0.0665	-0.458	-1.598	3.9605
7	5.8681	-1.9294	-0.7576	2.5528	1.5893	1.0341	0.1035	0.0626	0.2399	0.0452	0.0274	-0.2763	-0.1169	-0.1812	-0.1309	0.0231	0.004	0.0028	-0.0182	0.0167	-0.0286	10.272	-10.3847	11.372
8	0.3087	-1.0568	-1.7428	3.6175	5.9657	9.8382	0.4554	0.2121	0.1859	-0.188	-0.2374	0.0192	0.18	-0.5123	-0.2179	-0.0662	0.0062	-0.0073	0.0031	-0.0228	0.1022	-13.6226	6.5415	10.1803
9	12.3534	-1.6704	1.0023	1.2527	1.375	2.3033	-0.2883	-0.5165	-0.3693	0.3135	-0.0131	0.2562	-0.0344	-0.1012	0.3015	0.0232	-0.0348	0.0337	-0.0214	0.0592	0.0321	-12.1749	5.1515	24.3527
10	3.301	-0.3309	0.3633	0.0332	-0.0364	0.04	0.0212	0.1788	0.0532	0.1378	-0.2025	0.0294	0.0452	-0.2219	0.1813	0.0601	0.0007	0.0272	-0.0507	0.0231	0.0041	-10.4904	7.5421	17.907
11	4.9752	4.394	0.1937	9.6694	2.1314	7.3115	0.1617	0.2138	-0.2174	0.5526	0.2288	-0.1192	0.5274	0.38	-0.3905	-0.0608	0.0416	-0.033	-0.0232	-0.0757	0.0256	23.6702	-7.7976	21.2449
12	13.2377	-7.0288	-4.2368	21.3076	9.6298	8.0468	-0.4454	0.1662	-0.0415	0.2914	0.3544	0.562	-0.2479	0.4004	0.091	-0.0305	-0.0252	-0.0263	-0.0402	0.0606	-0.0539	22.0795	6.0322	24.8866
13	0.4373	0.1186	0.5109	4.7606	3.1573	2.752	-0.0688	-0.0587	-0.0352	0.0978	0.3042	-0.3041	0.1032	0.4443	-0.2354	-0.0024	0.0172	-0.0275	-0.02	0.0004	0.0231	20.8932	-0.2639	25.0813
14	4.0152	-1.6866	-3.3702	1.6865	-0.4717	6.4712	-0.0172	0.0556	0.0015	0.0208	0.0009	0.2011	0.455	0.148	0.0163	0.0071	-0.0262	0.0014	-0.0099	-0.017	-0.0071	-4.3625	-4.1147	14.5064
15	6.6046	-2.2282	-2.508	2.0896	3.6185	6.6975	0.1387	0.6211	0.0612	-0.1032	-0.3285	-0.1013	-0.3752	-0.3916	0.1898	0.0308	0.024	0.0216	0.0421	-0.0032	-0.0813	15.0713	0.0694	12.3735
16	1.1476	-0.3321	0.7035	0.0961	-0.2036	0.4313	-0.0354	-0.1449	0.1786	-0.052	0.0326	-0.0827	-0.0178	-0.1637	0.0029	0.0318	0.0003	-0.0008	-0.0026	0.0192	0.0048	-3.8243	9.9338	19.6344
17	1.3526	-0.4443	2.108	6.2201	1.4584	4.0467	-0.2703	-0.2648	-0.2845	0.0616	0.2304	-0.0928	-0.1996	0.1299	0.0399	-0.008	0.0383	-0.0194	0.0061	-0.003	0.0007	13.6561	-0.0785	27.2798

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	B	B	6 - 10	6 - 10
7	X-RAY DIFFRACTION	4	A	A	23 - 32	23 - 32
8	X-RAY DIFFRACTION	5	B	B	23 - 32	23 - 32
9	X-RAY DIFFRACTION	6	A	A	44 - 55	44 - 55
10	X-RAY DIFFRACTION	7	B	B	44 - 55	44 - 55
11	X-RAY DIFFRACTION	8	A	A	58 - 62	58 - 62
12	X-RAY DIFFRACTION	9	A	A	63 - 68	63 - 68
13	X-RAY DIFFRACTION	10	A	A	69 - 76	69 - 76
14	X-RAY DIFFRACTION	11	B	B	58 - 62	58 - 62
15	X-RAY DIFFRACTION	12	B	B	63 - 68	63 - 68
16	X-RAY DIFFRACTION	13	B	B	69 - 76	69 - 76
17	X-RAY DIFFRACTION	14	A	A	77 - 85	77 - 85
18	X-RAY DIFFRACTION	15	B	B	77 - 85	77 - 85
19	X-RAY DIFFRACTION	16	A	A	86 - 93	86 - 93
20	X-RAY DIFFRACTION	17	B	B	86 - 93	86 - 93

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