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

ID or keywords:

Entry

Database: PDB / ID: 2nxl

Title

Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide GLY-ALA-GLU-VAL-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

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

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: Refinement description / Category: software
Revision 1.3	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 1.4	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	2nxl.cif.gz	57 KB	Display	PDBx/mmCIF format
PDB format	pdb2nxl.ent.gz	42.2 KB	Display	PDB format
PDBx/mmJSON format	2nxl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	2nxdC 2nxmC 1t3rS 1kjg C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6dh7-d 2psv-d 1mtb-d 4q1x-d 4obh-2 6pjf-d 4q1y-d 4f75-d 4dqb-d 2fgu-d 3o9b-d 3o9d-d 4hvp-d 3ekt-2 1ec1-d 2nxd-d 2qi7-d 3r4b-d 3bgc-d 2rkg-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

hetero molecules

22.8 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)	50.861, 57.500, 61.887
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 1Subtypes of HIV / 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: 1027.085 Da / Num. of mol.: 1 / Fragment: decapeptide fragment / Mutation: TP2V / Source method: obtained synthetically Details: This sequence was custom-designed and then purchased commercially
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 137 / 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: 38.37 %
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 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 11, 2005 / Details: Yale mirrors
Radiation	Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→42.11 Å / Num. all: 12332 / Num. obs: 12332 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / R_merge(I) obs: 0.071 / R_sym value: 0.071 / Net I/σ(I): 12.5

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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→42.11 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.948 / SU B: 7.552 / SU ML: 0.113 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.216	608	4.9 %	RANDOM
R_work	0.16035	-	-	-
all	0.16307	11693	-	-
obs	0.16307	11693	95.92 %	-

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: 37.719 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.08 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-1.09 Å²

Refinement step

Cycle: LAST / Resolution: 2→42.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1565	0	10	137	1712

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	1604
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1541
X-RAY DIFFRACTION	r_angle_refined_deg	1.455	1.985	2192
X-RAY DIFFRACTION	r_angle_other_deg	0.781	3	3574
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.659	5	208
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.41	25.172	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.77	15	259
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.352	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	261
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1774
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	285
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	228
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	1499
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	740
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	1039
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	96
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	0.169	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.206	0.2	59
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.16	0.2	20
X-RAY DIFFRACTION	r_symmetry_hbond_other	0.05	0.2	1
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.723	1.5	1332
X-RAY DIFFRACTION	r_mcbond_other	0.152	1.5	437
X-RAY DIFFRACTION	r_mcangle_it	0.897	2	1674
X-RAY DIFFRACTION	r_scbond_it	1.411	3	641
X-RAY DIFFRACTION	r_scangle_it	2.1	4.5	518
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.049 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.251	39	-
R_work	0.181	794	-
obs	-	-	89.09 %

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	4.1613	1.19	-0.0977	4.7898	-0.6822	1.9913	-0.0855	0.2824	-0.2185	-0.0923	0.0476	-0.016	0.1054	-0.0132	0.0379	-0.0928	-0.0203	0.007	-0.1101	-0.0288	-0.1761	21.5393	2.6079	1.7631
2	2.4426	1.3591	0.2987	1.9363	1.69	6.5669	-0.1409	0.0114	0.2098	-0.0761	0.0636	0.151	-0.185	-0.0674	0.0773	-0.1375	0.0031	-0.0162	-0.1547	0.0068	-0.1137	20.0044	10.8297	7.1886
3	18.433	0.8965	7.4251	6.6918	-0.5578	7.3095	0.0489	-0.0158	-0.3153	-0.0973	0.0182	-0.8887	0.1877	0.5326	-0.0671	-0.0568	0.0082	0.0302	-0.0332	0.0214	-0.0003	39.2493	-2.0775	7.9964
4	5.6554	-3.5852	1.6907	5.056	-1.298	1.0005	-0.0057	0.2022	-0.1427	-0.2939	0.0692	0.0076	-0.2353	-0.0489	-0.0635	-0.1276	-0.0442	0.0185	-0.1225	0.0005	-0.1063	26.9019	1.3742	12.4345
5	10.1051	-2.2041	0.109	7.2526	5.0434	12.3904	0.1956	-0.1927	-0.1447	0.0487	0.0489	-0.4149	0.538	0.7532	-0.2445	-0.195	0.0241	0.0104	-0.0437	0.0735	-0.1298	39.6702	-1.479	20.9764
6	22.864	1.2065	1.2558	13.1294	2.5848	14.5025	0.3762	-0.3126	-0.2726	0.3877	-0.6189	0.7986	0.3325	-0.9547	0.2427	-0.1652	-0.0098	0.0092	-0.1417	-0.0478	-0.1001	2.5048	7.3453	12.5913
7	8.7549	-3.1181	-3.43	1.963	0.8877	3.9514	-0.0476	-0.2405	0.2987	-0.0572	0.0499	-0.0209	0.0581	0.1451	-0.0023	-0.1512	0	-0.0072	-0.1043	0.0155	-0.1122	14.0099	1.7359	11.8877
8	10.1655	1.6512	1.0375	12.6864	6.0209	5.456	0.063	-0.2364	0.421	0.0711	-0.3162	0.8262	-0.2502	-0.5086	0.2532	-0.1906	0.0126	-0.0189	-0.1127	0.0574	-0.1305	0.4528	-4.5983	17.5351
9	29.2617	0.8123	9.779	5.0334	-0.0268	9.845	0.1639	0.075	0.5069	0.1412	0.0494	0.185	-0.0738	-0.012	-0.2133	-0.0871	0.0002	0.0235	-0.1646	0.0117	-0.1903	26.0332	-1.0503	26.4696
10	18.9862	4.1421	1.7908	4.5755	-0.382	4.2101	-0.0758	-0.1204	0.4887	0.2561	-0.1553	0.0817	-0.2963	0.0911	0.2311	-0.1275	0.0144	-0.0004	-0.1733	0.0244	-0.1346	14.1679	-9.8904	19.5789
11	8.6203	8.4468	-9.0932	10.1457	-13.6281	21.5021	0.2999	-0.621	-0.038	-0.1534	-0.7505	-0.328	0.317	1.214	0.4506	-0.2053	0.0089	-0.0336	-0.0629	-0.023	-0.0756	38.7317	4.4089	21.6592
12	42.4718	5.0136	16.9048	10.1071	3.9615	7.1347	0.2494	0.9754	-1.3137	-0.2191	0.0016	0.3085	-0.5015	0.2619	-0.251	-0.1608	0.0183	0.0523	-0.0769	-0.0687	-0.0494	37.5847	4.7478	7.3618
13	3.8555	1.0497	1.124	2.073	1.0743	0.6579	0.1463	-0.1275	-0.0413	0.0689	-0.2585	-0.0969	-0.1131	0.4592	0.1122	-0.1453	0.0112	-0.0104	-0.1282	-0.0233	-0.0759	36.1293	7.3098	13.5478
14	6.0389	-4.2858	1.0593	5.0374	-4.7721	14.589	0.374	0.0752	-0.4174	-0.2335	0.142	-0.0114	0.3701	-0.2938	-0.5159	-0.1479	-0.041	-0.0055	-0.1165	0.05	-0.0496	1.688	-7.5461	12.0842
15	41.3971	25.1247	-3.1847	21.2196	-5.8122	3.4846	0.0911	-0.962	0.5399	-0.3029	0.175	0.0033	0.0552	0.2428	-0.2662	-0.0685	0.0155	0.016	-0.0206	-0.1146	-0.0942	3.806	5.367	5.9527
16	1.3466	0.1535	0.8851	3.5171	-2.8779	5.1037	-0.0088	0.0119	-0.0619	0.2496	0.2317	0.6188	-0.1139	-0.1119	-0.2229	-0.1386	-0.0116	0.032	-0.0895	-0.0108	-0.041	4.4725	-0.7224	5.8424
17	0.1903	-0.0879	1.1901	7.0674	-4.1341	9.2727	0.059	-0.132	-0.1245	-0.1567	0.0454	0.283	0.4565	-0.079	-0.1044	-0.1359	0.0144	0.018	-0.0769	0.0151	-0.0453	29.7474	-3.782	16.6103
18	9.4677	4.3625	-4.543	5.8763	-2.0996	2.1799	0.4197	-0.5352	0.0175	0.4736	-0.3159	-0.0553	-0.0426	0.2472	-0.1038	-0.1423	-0.0326	-0.0084	-0.0776	0.0205	-0.1103	10.3509	0.2545	18.1734
19	2.4264	2.2162	0.1931	3.4009	-0.3645	1.0198	0.0774	0.0469	0.1476	0.0282	-0.0336	-0.1103	0.0847	0.0803	-0.0438	-0.1092	-0.0162	0.0053	-0.0733	0.0037	-0.093	29.1449	9.2966	11.1696
20	9.9528	2.8515	2.6392	2.4782	-2.1766	5.8774	-0.3621	0.4571	-0.2469	0.0346	0.5788	0.2666	0.0013	-0.1214	-0.2167	-0.1128	-0.0231	-0.0133	-0.138	0.0026	-0.1193	12.2174	-0.1497	3.8837

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

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Jul 12, 2017. Major update of PDB

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Yorodumi