PDB-3lin: crystal structure of HTLV protease complexed with the inhibitor, ...

ID or keywords:

Entry

Database: PDB / ID: 3lin

Title

crystal structure of HTLV protease complexed with the inhibitor, KNI-10562

Components

Protease

Keywords

HYDROLASE/HYDROLASE INHIBITOR /

HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

aspartic-type endopeptidase activity /

proteolysis /

metal ion binding
Similarity search - Function

Biological species

Human T-lymphotropic virus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Satoh, T. / Li, M. / Nguyen, J. / Kiso, Y. / Wlodawer, A. / Gustchina, A.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease.
Authors: Satoh, T. / Li, M. / Nguyen, J.T. / Kiso, Y. / Gustchina, A. / Wlodawer, A.

History

Deposition	Jan 25, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 14, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2	Dec 12, 2012	Group: Other
Revision 1.3	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Oct 13, 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	Sep 6, 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	3lin.cif.gz	563 KB	Display	PDBx/mmCIF format
PDB format	pdb3lin.ent.gz	469.6 KB	Display	PDB format
PDBx/mmJSON format	3lin.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/li/3lin ftp://data.pdbj.org/pub/pdb/validation_reports/li/3lin	HTTPS FTP

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Related structure data

Related structure data	3liqC 3litC 3livC 3lixC 3liyC 2b7fS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3liy-1 4ydf-d 3liq-d 3liy-3 6ga4-d 3lix-d 5ax1-d 2b7f-3 2b7f-1 3liy-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protease

B: Protease

C: Protease

D: Protease

E: Protease

F: Protease

G: Protease

H: Protease

I: Protease

J: Protease

K: Protease

L: Protease

hetero molecules

155 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protease

B: Protease

hetero molecules

defined by author&software
25.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Protease

D: Protease

hetero molecules

defined by author&software
25.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Protease

F: Protease

hetero molecules

defined by author&software
25.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Protease

H: Protease

hetero molecules

defined by author&software
25.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Protease

J: Protease

hetero molecules

defined by author&software
25.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Protease

L: Protease

hetero molecules

defined by author&software
25.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.360, 77.308, 159.170
Angle α, β, γ (deg.)	90.00, 95.09, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID
1
2
3
4
5
6

Details

Homodimer contain chain C and D and inhibitor N / Homodimer contains chain E and F and inhibitor O / Homodimer contains chain G and H and inhibitor P / Homodimer contains chain I and J and inhibitor Q / Homodimer contains chain K and L and inhibitor R

#1: Protein	Protease / Mass: 12566.579 Da / Num. of mol.: 12 / Mutation: L40I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human T-lymphotropic virus 1 / Gene: prt / Plasmid: pHTLVdelta9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q82134
#2: Chemical	ChemComp-E13 / N-[(2S,3S)-4-{(4R)-4-[(2,2-dimethylpropyl)carbamoyl]-5,5-dimethyl-1,3-thiazolidin-3-yl}-3-hydroxy-4-oxo-1-phenylbutan-2-yl]-N~2~-{(2S)-2-[(methoxycarbonyl)amino]-2-phenylacetyl}-3-methyl-L-valinamide / KNI-10562 Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 711.911 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₇H₅₃N₅O₇S / References: KNI-10562
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.73 Å³/Da / Density % sol: 54.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 26% Pentaerythritol ethoxylate, 0.2M ZnSO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2008
Radiation	Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.96→50 Å / Num. obs: 112737 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / R_sym value: 0.087 / Net I/σ(I): 24.9
Reflection shell	Resolution: 1.96→2.03 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.1 / R_sym value: 0.305 / % possible all: 79.3

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
REFMAC	5.5.0104	refinement
HKL-3000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2B7F

2b7f

Resolution: 1.96→50 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.924 / SU B: 9.456 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26225	3393	3 %	RANDOM
R_work	0.21297	-	-	-
obs	0.21438	109344	96.9 %	-

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: 26.448 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.18 Å²	0 Å²	-0.54 Å²
2-	-	-2.1 Å²	0 Å²
3-	-	-	3.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10595	0	300	785	11680

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	11353
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.785	2.036	15622
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.714	5	1404
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.615	24.468	376
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.773	15	1822
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.947	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	1908
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.022	8294
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	5.433	2	7109
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	7.213	3	11759
X-RAY DIFFRACTION	r_scbond_it	9.02	2	4244
X-RAY DIFFRACTION	r_scangle_it	11.118	3	3842
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	851	medium positional	0.5	0.5
1	1	B	851	medium positional	0.46	0.5
1	1	C	851	medium positional	0.48	0.5
1	1	D	851	medium positional	0.42	0.5
1	1	E	851	medium positional	0.5	0.5
1	1	F	851	medium positional	0.41	0.5
1	1	G	851	medium positional	0.46	0.5
1	1	H	851	medium positional	0.4	0.5
1	1	I	851	medium positional	0.42	0.5
1	1	J	851	medium positional	0.33	0.5
1	1	K	851	medium positional	0.41	0.5
1	1	L	851	medium positional	0.33	0.5
2	2	C	851	medium positional	0.5	0.5
2	2	D	851	medium positional	0.38	0.5
2	2	B	851	medium positional	0.4	0.5
2	2	F	851	medium positional	0.35	0.5
2	2	G	851	medium positional	0.48	0.5
2	2	H	851	medium positional	0.35	0.5
2	2	I	851	medium positional	0.44	0.5
2	2	J	851	medium positional	0.36	0.5
2	2	K	851	medium positional	0.42	0.5
2	2	L	851	medium positional	0.42	0.5
3	3	E	851	medium positional	0.52	0.5
3	3	F	851	medium positional	0.37	0.5
3	3	B	851	medium positional	0.41	0.5
3	3	D	851	medium positional	0.37	0.5
3	3	G	851	medium positional	0.48	0.5
3	3	H	851	medium positional	0.35	0.5
3	3	I	851	medium positional	0.45	0.5
3	3	J	851	medium positional	0.37	0.5
3	3	K	851	medium positional	0.38	0.5
4	4	G	851	medium positional	0.51	0.5
4	4	H	851	medium positional	0.3	0.5
4	4	B	851	medium positional	0.39	0.5
4	4	D	851	medium positional	0.35	0.5
4	4	F	851	medium positional	0.35	0.5
4	4	H	851	medium positional	0.3	0.5
4	4	I	851	medium positional	0.47	0.5
4	4	J	851	medium positional	0.35	0.5
4	4	K	851	medium positional	0.43	0.5
5	5	I	851	medium positional	0.51	0.5
5	5	J	851	medium positional	0.33	0.5
5	5	B	851	medium positional	0.35	0.5
5	5	D	851	medium positional	0.33	0.5
5	5	F	851	medium positional	0.32	0.5
5	5	H	851	medium positional	0.28	0.5
5	5	L	851	medium positional	0.36	0.5
6	6	K	864	medium positional	0.47	0.5
6	6	L	864	medium positional	0.36	0.5
6	6	B	864	medium positional	0.36	0.5
6	6	D	864	medium positional	0.32	0.5
6	6	F	864	medium positional	0.34	0.5
6	6	H	864	medium positional	0.28	0.5
6	6	J	864	medium positional	0.34	0.5
1	1	A	851	medium thermal	1.66	2
1	1	B	851	medium thermal	0.74	2
1	1	C	851	medium thermal	1.09	2
1	1	D	851	medium thermal	0.67	2
1	1	E	851	medium thermal	1.34	2
1	1	F	851	medium thermal	0.63	2
1	1	G	851	medium thermal	0.63	2
1	1	H	851	medium thermal	0.65	2
1	1	I	851	medium thermal	0.7	2
1	1	J	851	medium thermal	0.42	2
1	1	K	851	medium thermal	0.63	2
1	1	L	851	medium thermal	0.42	2
2	2	C	851	medium thermal	1.17	2
2	2	D	851	medium thermal	0.57	2
2	2	B	851	medium thermal	0.57	2
2	2	F	851	medium thermal	0.5	2
2	2	G	851	medium thermal	0.71	2
2	2	H	851	medium thermal	0.52	2
2	2	I	851	medium thermal	0.75	2
2	2	J	851	medium thermal	0.5	2
2	2	K	851	medium thermal	0.53	2
2	2	L	851	medium thermal	1.01	2
3	3	E	851	medium thermal	1.33	2
3	3	F	851	medium thermal	0.54	2
3	3	B	851	medium thermal	0.63	2
3	3	D	851	medium thermal	0.57	2
3	3	G	851	medium thermal	0.69	2
3	3	H	851	medium thermal	0.54	2
3	3	I	851	medium thermal	0.67	2
3	3	J	851	medium thermal	0.56	2
3	3	K	851	medium thermal	0.52	2
4	4	G	851	medium thermal	0.73	2
4	4	H	851	medium thermal	0.43	2
4	4	B	851	medium thermal	0.56	2
4	4	D	851	medium thermal	0.52	2
4	4	F	851	medium thermal	0.49	2
4	4	H	851	medium thermal	0.43	2
4	4	I	851	medium thermal	0.73	2
4	4	J	851	medium thermal	0.49	2
4	4	K	851	medium thermal	0.55	2
5	5	I	851	medium thermal	0.8	2
5	5	J	851	medium thermal	0.48	2
5	5	B	851	medium thermal	0.47	2
5	5	D	851	medium thermal	0.52	2
5	5	F	851	medium thermal	0.45	2
5	5	H	851	medium thermal	0.46	2
5	5	L	851	medium thermal	0.88	2
6	6	K	864	medium thermal	0.67	2
6	6	L	864	medium thermal	0.9	2
6	6	B	864	medium thermal	0.49	2
6	6	D	864	medium thermal	0.54	2
6	6	F	864	medium thermal	0.46	2
6	6	H	864	medium thermal	0.51	2
6	6	J	864	medium thermal	0.5	2

LS refinement shell

Resolution: 1.962→2.013 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	230	-
R_work	0.248	6167	-
obs	-	-	74.84 %

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	4.3662	1.0411	-0.4868	1.8393	-0.1819	0.2767	0.0537	0.2173	-0.052	0.0029	-0.0743	0.1797	-0.0063	-0.0436	0.0206	0.0959	0.0292	-0.0022	0.1344	-0.0394	0.0623	26.5052	6.9256	58.5192
2	1.441	0.8889	0.239	3.6243	0.5711	0.5251	-0.1115	0.0452	0.0919	-0.01	0.087	-0.1852	-0.0105	0.0123	0.0245	0.0917	-0.0066	-0.0208	0.1167	0.0175	0.0333	-6.997	26.0585	58.5415
3	2.6586	-1.1322	0.0981	2.1409	0.3288	0.2849	0.0148	-0.0504	0.1787	-0.0723	-0.0333	0.0663	-0.0555	-0.0465	0.0185	0.1185	0.003	0.0194	0.1034	0.0115	0.0331	26.326	44.9637	58.3875
4	3.3183	-0.3707	-0.4692	1.3883	0.1458	0.3565	0.0554	-0.0799	0.0719	-0.0591	-0.0905	-0.189	-0.0232	0.011	0.0351	0.0992	-0.0081	0.0112	0.1184	0.047	0.0522	33.754	33.218	20.698
5	1.4613	-0.6075	-0.095	3.6124	0.0192	0.2938	-0.0793	-0.0231	-0.108	0.0073	0.0738	-0.0118	0.0372	0.0221	0.0056	0.0974	0.0192	-0.001	0.119	0.004	0.0097	66.7334	52.5306	20.8565
6	3.4004	1.8912	0.392	2.9886	0.121	0.2551	0.0874	-0.0335	-0.1486	0.2556	-0.0807	-0.0082	0.0229	0.0146	-0.0067	0.1366	0.0094	0.0394	0.091	-0.0034	0.037	33.8035	71.5457	20.7659

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 116
2	X-RAY DIFFRACTION	1	B	1 - 116
3	X-RAY DIFFRACTION	2	C	1 - 116
4	X-RAY DIFFRACTION	2	D	1 - 116
5	X-RAY DIFFRACTION	3	E	1 - 116
6	X-RAY DIFFRACTION	3	F	1 - 116
7	X-RAY DIFFRACTION	4	G	1 - 116
8	X-RAY DIFFRACTION	4	H	1 - 116
9	X-RAY DIFFRACTION	5	I	1 - 116
10	X-RAY DIFFRACTION	5	J	1 - 116
11	X-RAY DIFFRACTION	6	K	1 - 116
12	X-RAY DIFFRACTION	6	L	1 - 116

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Yorodumi