PDB-2ydf: HUMAN SERUM ALBUMIN COMPLEXED WITH IOPHENOXIC ACID

ID or keywords:

Entry

Database: PDB / ID: 2ydf

Title

HUMAN SERUM ALBUMIN COMPLEXED WITH IOPHENOXIC ACID

Components

SERUM ALBUMIN

Keywords

TRANSPORT PROTEIN

Function / homology

Function and homology information

exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Ryan, A.J. / Curry, S.

Citation

Journal: Bmc Struct.Biol. / Year: 2011
Title: Crystallographic Analysis Reveals the Structural Basis of the High-Affinity Binding of Iophenoxic Acid to Human Serum Albumin.
Authors: Ryan, A.J. / Chung, C.W. / Curry, S.

History

Deposition	Mar 18, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2ydf.cif.gz	398.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2ydf.ent.gz	326 KB	Display	PDB format
PDBx/mmJSON format	2ydf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2ydf_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	2ydf_full_validation.pdf.gz	2.7 MB	Display
Data in XML	2ydf_validation.xml.gz	41.1 KB	Display
Data in CIF	2ydf_validation.cif.gz	54.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yd/2ydf ftp://data.pdbj.org/pub/pdb/validation_reports/yd/2ydf	HTTPS FTP

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Related structure data

Related structure data	2bxaS 1ao6 1bj5 1bke 1bm0 1e78 1e7a 1e7b 1e7c 1e7e 1e7f 1e7g 1e7h 1e7i 1gni 1gnj 1h9z 1ha2 1hk1 1hk2 1hk3 1hk4 1hk5 1n5u 1o9x 1tf0 1uor 1ysx 2bx8 2bxb 2bxc 2bxd 2bxe 2bxf 2bxg 2bxh 2bxi 2bxk 2bxl 2bxm 2bxn 2bxo 2bxp 2bxq 2esg 2vdb 2vue 2vuf 2xsi 2xvq 2xvu 2xvv 2xvw 2xw0 2xw1 S: Starting model for refinement
Similar structure data	5hoz-d 4zbq-d 2xvq-2 5id9-d 5dby-d 2bxd-1 3lu8-2 6u5a-d 2bxe-2 5okl-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#37 - Jan 2003 Serum Albumin similarity (15) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (15) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (10) #155 - Nov 2012 Vitamin D Receptor similarity (9) #41 - May 2003 Hemoglobin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (2) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #136 - Apr 2011 Nanobodies similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #21 - Sep 2001 Antibodies similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#37 - Jan 2003
Serum Albumin
similarity (15)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (15)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (10)
#155 - Nov 2012
Vitamin D Receptor
similarity (9)
#41 - May 2003
Hemoglobin
similarity (1)
#237 - Sep 2019
Nanodiscs and HDL
similarity (2)
#206 - Feb 2017
Globin Evolution
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#136 - Apr 2011
Nanobodies
similarity (1)
#159 - Mar 2013
Erythrocruorin
similarity (1)
#21 - Sep 2001
Antibodies
similarity (1)

Deposited unit

A: SERUM ALBUMIN

B: SERUM ALBUMIN

hetero molecules

138 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SERUM ALBUMIN

hetero molecules

defined by software
68.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: SERUM ALBUMIN

hetero molecules

defined by software
68.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.072, 55.440, 119.845
Angle α, β, γ (deg.)	81.00, 90.83, 64.52
Int Tables number	1
Space group name H-M	P1

#1: Protein	SERUM ALBUMIN Mass: 66571.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD SERUM / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02768
#2: Chemical	ChemComp-IO3 / IOPHENOXIC ACID Mass: 571.917 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₁H₁₁I₃O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.6 Å³/Da / Density % sol: 53 % / Description: NONE
Crystal grow	pH: 7 / Details: SEE PAPER, pH 7

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Data collection

Diffraction	Mean temperature: 298 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2007 / Details: MIRRORS
Radiation	Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.488 Å / Relative weight: 1
Reflection	Resolution: 2.75→59 Å / Num. obs: 31655 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / B_iso Wilson estimate: 65.63 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.75→2.9 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.34 / Mean I/σ(I) obs: 1.7 / % possible all: 92.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BXA

2bxa

Resolution: 2.75→35.124 Å / SU ML: 0.38 / σ(F): 1.98 / Phase error: 25.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2393	1468	4.7 %
R_work	0.2066	-	-
obs	0.2081	30955	94.69 %

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.648 Å² / k_sol: 0.311 e/Å³

Displacement parameters

B_iso mean: 42.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	43.0395 Å²	-7.2816 Å²	5.4319 Å²
2-	-	45.6746 Å²	-3.1258 Å²
3-	-	-	32.5483 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→35.124 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8283	0	136	23	8442

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8611
X-RAY DIFFRACTION	f_angle_d	0.599	11699
X-RAY DIFFRACTION	f_dihedral_angle_d	12.109	2992
X-RAY DIFFRACTION	f_chiral_restr	0.043	1365
X-RAY DIFFRACTION	f_plane_restr	0.005	1529

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.75-2.8482	0.3467	131	0.288	2868	X-RAY DIFFRACTION	93
2.8482-2.9622	0.2847	142	0.2735	2905	X-RAY DIFFRACTION	93
2.9622-3.097	0.3294	147	0.2752	2778	X-RAY DIFFRACTION	89
3.097-3.2601	0.278	141	0.2419	2929	X-RAY DIFFRACTION	94
3.2601-3.4642	0.2624	162	0.2155	2985	X-RAY DIFFRACTION	96
3.4642-3.7314	0.253	149	0.2103	2962	X-RAY DIFFRACTION	96
3.7314-4.1064	0.2311	154	0.1916	2968	X-RAY DIFFRACTION	96
4.1064-4.6994	0.2008	148	0.1732	3028	X-RAY DIFFRACTION	97
4.6994-5.9162	0.2255	151	0.1952	3036	X-RAY DIFFRACTION	97
5.9162-35.1271	0.2175	143	0.1984	3028	X-RAY DIFFRACTION	97

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	0.312	-0.1832	-0.0609	0.4445	0.5038	0.6639	-0.0475	-0.07	-0.0758	0.1484	-0.0145	0.071	0.1892	-0.0548	-0.3004	0.1228	0.0025	0.1238	0.1125	-0.0101	-0.0768	-14.2389	-2.4416	22.6418
2	0.6402	0.0855	-1.0455	0.7718	-0.3714	1.7788	-0.0051	-0.0015	-0.1324	0.2958	-0.1752	0.292	0.1706	-0.3718	0.0919	0.4003	-0.1002	0.1207	0.4155	-0.0875	0.3607	-22.6451	-2.7874	10.8986
3	0.4288	-0.3342	-0.2644	0.7665	-0.3149	0.6997	-0.0119	0.0574	0.09	-0.0895	-0.0863	0.0781	-0.3226	-0.1044	-0.0259	0.3006	0.0845	-0.03	0.123	-0.0194	0.0858	-6.081	14.7395	5.8498
4	0.222	0.0601	-0.0873	0.0712	0.015	0.3032	0.0454	-0.1044	0.1123	0.0507	-0.0326	-0.0356	-0.0878	0.0506	-1.0745	0.0564	-0.1186	0.0969	0.0557	-0.2968	-0.1389	2.3324	8.4535	14.4373
5	0.0119	0.0029	-0.001	0.0021	0.001	0.0025	0.0121	-0.0022	-0.017	0.0202	0.0082	-0.0161	0.0144	-0.0005	0.0246	-0.0255	-0.0633	-0.044	-0.0486	0.0371	-0.044	2.4004	-17.7916	1.7521
6	0.0183	-0.0209	-0.0043	0.1861	0.1221	0.0837	0.0495	-0.02	-0.05	0.1565	0.0355	-0.0861	0.1037	0.0131	0.9643	0.1166	-0.0314	-0.133	0.0188	-0.0497	-0.0073	6.9495	-17.7136	6.845
7	0.0086	-0.0026	0.0002	0.0014	-0.0005	0.0009	-0.0064	0.0107	-0.0142	-0.0008	-0.0088	0.006	0.013	0.002	-0.032	-0.066	-0.0844	-0.0809	-0.1108	-0.1151	-0.0245	6.1481	-23.012	-11.1546
8	0.0144	-0.0118	0.0152	0.0037	-0.0084	0.0092	-0.0695	0.0228	-0.0126	0.0047	-0.0062	-0.0578	-0.0267	-0.0192	-1.0548	-0.2102	-0.1972	-0.1948	-0.2478	-0.1332	-0.2437	4.7574	-1.0999	-14.9061
9	0.5183	0.0034	0.5935	-0.0011	0.0048	0.6752	-0.4106	-0.3852	0.3544	-0.42	0.0334	0.1753	-0.7676	-0.4347	0.5582	0.458	0.165	-0.1938	0.3149	-0.1467	0.3284	-2.4559	25.7656	-12.1814
10	1.6043	0.2095	1.3342	0.6514	0.651	2.1712	-0.1683	-0.0685	0.2299	-0.0666	-0.0667	0.0936	-0.218	-0.0885	0.1395	0.025	-0.0043	-0.0551	-0.0483	-0.0569	0.0386	0.5157	19.7144	-14.8472
11	3.3701	-0.0141	0.635	0.8888	-0.6498	2.4831	-0.1914	0.034	0.5209	0.2902	-0.1028	-0.221	-0.3376	0.1115	0.2663	0.2279	-0.1336	-0.152	0.1891	0.1328	0.2124	6.6796	25.6627	-19.6817
12	0.5921	-0.1895	0.3491	0.0673	-0.0986	0.23	-0.112	-0.2103	0.0072	0.0496	0.0552	0.0342	-0.0714	-0.1027	0.0434	1.5511	-0.1732	-0.2071	2.5442	0.8903	2.1544	0.2704	36.2063	-17.1574
13	0.4493	0.0147	-0.6804	0.2759	0.0543	1.0517	0.0109	0.1751	-0.0048	-0.0416	-0.0126	0.0741	-0.0423	-0.2636	-0.2277	0.0499	-0.0092	0.0326	0.1243	-0.0443	-0.029	44.1474	18.273	39.2884
14	0.2403	-0.0247	0.085	0.0024	-0.0015	0.4494	-0.064	0.4661	-0.2318	-0.0932	0.0284	0.0435	0.0521	-0.1858	0.0494	0.2234	-0.1095	0.0731	0.6291	-0.272	0.3264	44.7196	12.1891	34.3697
15	2.7874	-0.0133	1.4886	2.3529	0.3343	0.8445	0.2406	0.0446	-0.3022	-0.7178	0.3256	0.2472	0.216	-0.685	-0.5314	1.0835	-0.3981	-0.1208	1.2739	-0.0043	0.4113	34.9258	16.7769	25.984
16	0.5737	0.2026	0.1725	0.1965	0.183	0.1917	-0.2044	0.3726	-0.1069	-0.1317	0.0876	0.037	0.1181	-0.1794	-0.16	0.1712	-0.1353	0.0862	0.3269	-0.1139	0.1098	47.0428	13.6658	44.0011
17	0.0261	-0.0859	-0.0635	0.295	0.2861	0.6145	0.0237	0.0125	0.0681	-0.0974	0.0691	-0.1697	-0.1361	0.2138	-0.1963	0.0033	-0.0808	0.2497	0.1066	-0.1731	-0.0661	58.2507	27.2095	45.9083
18	0.6527	-0.0743	-0.2829	0.1352	0.1022	0.3763	0.0513	0.261	0.1475	-0.1026	-0.025	-0.0031	-0.0743	-0.0962	0.998	-0.0843	-0.0492	0.1337	0.0858	0.1052	-0.167	38.2426	36.8514	50.6056
19	0.7507	-0.0696	-0.5628	0.0225	0.041	0.4385	0.0036	0.051	0.0171	-0.0621	-0.005	-0.0583	0.0007	-0.0171	-0.3243	0.1452	-0.0276	0.1201	0.1332	0.0286	0.1794	30.802	49.3003	64.7875
20	0.0032	-0.0115	0.0017	-0.0027	-0.0202	-0.003	0.0356	0.0046	0.1014	0.0338	-0.0274	0.0273	0.0093	-0.0243	1.9531	-0.2982	-0.0752	0.2771	-0.1663	0.088	-0.2084	46.2926	35.0758	73.1215
21	0.4116	0.1208	0.2719	0.0813	0.1562	0.3055	0.1026	0.1041	-0.1035	-0.2636	-0.0688	-0.2388	-0.0029	0.2678	0.1078	0.496	0.1775	0.2649	0.4749	0.062	0.5773	71.9382	13.2771	72.6284
22	2.9249	-0.2705	-2.3006	0.6107	0.4453	2.2712	-0.0884	-0.127	-0.1595	-0.0096	-0.0525	-0.0266	0.134	0.1391	0.0808	0.0073	0.0533	0.0347	0.041	0.0253	0.0385	66.8708	19.7684	74.6396
23	0.9339	-0.7289	-0.8576	4.5002	0.6376	3.4925	0.2872	-0.1841	-0.0073	0.0138	-0.6393	-1.2998	-0.0649	0.5905	0.2025	0.3586	-0.1849	-0.0782	0.8076	0.3399	0.6359	75.7841	22.8288	79.3041
24	0.7778	0.5692	0.5948	1.6892	0.2648	0.4777	-0.0542	-0.837	-0.0028	0.3107	-0.2409	-1.0115	0.0426	-0.3594	0.2877	1.2888	-0.2126	-0.3364	2.4471	1.0003	2.2679	82.8745	12.7386	76.0171

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 5:63)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 64:106)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 107:119)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 120:201)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 202:240)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 241:321)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 322:364)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 365:497)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 498:519)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 520:536)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 537:560)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 561:582)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 5:38)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 39:50)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 51:56)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 57:133)
17	X-RAY DIFFRACTION	17	(CHAIN B AND RESID 134:196)
18	X-RAY DIFFRACTION	18	(CHAIN B AND RESID 197:289)
19	X-RAY DIFFRACTION	19	(CHAIN B AND RESID 290:324)
20	X-RAY DIFFRACTION	20	(CHAIN B AND RESID 325:497)
21	X-RAY DIFFRACTION	21	(CHAIN B AND RESID 498:518)
22	X-RAY DIFFRACTION	22	(CHAIN B AND RESID 519:537)
23	X-RAY DIFFRACTION	23	(CHAIN B AND RESID 538:559)
24	X-RAY DIFFRACTION	24	(CHAIN B AND RESID 560:582)

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