PDB-9zmd: Equine Serum Albumin with Copper(II)

ID or keywords:

Entry

Database: PDB / ID: 9zmd

Title

Equine Serum Albumin with Copper(II)

Components

Serum albumin

Keywords

METAL BINDING PROTEIN / TRANSPORT PROTEIN / COPPER / METAL BINDING / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / fatty acid binding / cellular response to starvation / pyridoxal phosphate binding / protein-containing complex / extracellular space / DNA binding ...
Similarity search - Function

Biological species

Equus caballus (horse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Handing, K.B. / Bijak, V. / Gucwa, M. / Slawek, J. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Equine Serum Albumin with Copper(II)
Authors: Handing, K.B. / Bijak, V. / Gucwa, M. / Slawek, J. / Minor, W. / Stewart, A.J.

History

Deposition	Dec 10, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9zmd.cif.gz	138.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9zmd.ent.gz	102.7 KB	Display	PDB format
PDBx/mmJSON format	9zmd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9zmd_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	9zmd_full_validation.pdf.gz	2.1 MB	Display
Data in XML	9zmd_validation.xml.gz	27.4 KB	Display
Data in CIF	9zmd_validation.cif.gz	37.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/9zmd ftp://data.pdbj.org/pub/pdb/validation_reports/zm/9zmd	HTTPS FTP

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Related structure data

Similar structure data	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	#258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (10) #37 - Jan 2003 Serum Albumin similarity (9) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (9) #155 - Nov 2012 Vitamin D Receptor similarity (8)

Deposited unit

A: Serum albumin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	93.428, 93.428, 141.752
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Serum albumin Mass: 65768.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.7 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 7.4, 2.2 M ammonium sulfate, 5 mM copper(II) chloride mixed 1:1 with 36 mg/mL protein, 10 mM Tris-HCl, 150 mM sodium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.28291 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 16, 2015
Radiation	Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.28291 Å / Relative weight: 1
Reflection	Resolution: 2.36→28 Å / Num. obs: 28717 / % possible obs: 98.8 % / Redundancy: 5.5 % / R_merge(I) obs: 0.081 / R_pim(I) all: 0.037 / Net I/σ(I): 17.7
Reflection shell	Resolution: 2.36→2.4 Å / Num. unique obs: 1291 / CC_1/2: 0.48

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-3000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→26.985 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.879 / SU B: 12.149 / SU ML: 0.252 / Cross valid method: FREE R-VALUE / ESU R Free: 0.344
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2513	1013	5.041 %
R_work	0.1913	19083	-
all	0.194	-	-
obs	-	20096	98.529 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 35.847 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.403 Å²	0.202 Å²	0 Å²
2-	-	0.403 Å²	-0 Å²
3-	-	-	-1.307 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→26.985 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4603	0	43	230	4876

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	4750
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4429
X-RAY DIFFRACTION	r_angle_refined_deg	1.067	1.869	6429
X-RAY DIFFRACTION	r_angle_other_deg	0.416	1.787	10319
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.209	5	584
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.457	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.296	10	856
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.28	10	215
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	708
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5390
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	976
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1195
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	3931
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2350
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.069	0.2	2385
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	167
X-RAY DIFFRACTION	r_metal_ion_refined	0.188	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.283	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.333	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.181	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	1.608	3.642	2336
X-RAY DIFFRACTION	r_mcbond_other	1.608	3.642	2336
X-RAY DIFFRACTION	r_mcangle_it	2.788	6.548	2920
X-RAY DIFFRACTION	r_mcangle_other	2.788	6.548	2921
X-RAY DIFFRACTION	r_scbond_it	1.935	3.957	2414
X-RAY DIFFRACTION	r_scbond_other	1.91	3.903	2387
X-RAY DIFFRACTION	r_scangle_it	3.39	7.181	3509
X-RAY DIFFRACTION	r_scangle_other	3.38	7.087	3468
X-RAY DIFFRACTION	r_lrange_it	6.68	36.484	5461
X-RAY DIFFRACTION	r_lrange_other	6.4	36.512	5438

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.65-2.718	0.314	55	0.255	1258	0.258	1492	0.949	0.964	88.0027	0.226
2.718-2.792	0.261	82	0.259	1337	0.259	1454	0.962	0.959	97.5928	0.216
2.792-2.872	0.357	60	0.262	1348	0.266	1421	0.925	0.957	99.0852	0.219
2.872-2.959	0.364	61	0.242	1286	0.246	1351	0.922	0.962	99.7039	0.204
2.959-3.055	0.281	73	0.221	1252	0.225	1326	0.947	0.968	99.9246	0.191
3.055-3.161	0.28	79	0.2	1214	0.205	1295	0.951	0.975	99.8456	0.172
3.161-3.278	0.294	79	0.206	1160	0.211	1240	0.942	0.974	99.9194	0.185
3.278-3.41	0.259	46	0.196	1151	0.198	1198	0.962	0.977	99.9165	0.179
3.41-3.559	0.273	52	0.198	1091	0.202	1143	0.958	0.978	100	0.187
3.559-3.73	0.224	67	0.17	1056	0.173	1124	0.97	0.983	99.911	0.161
3.73-3.927	0.228	57	0.154	993	0.158	1051	0.969	0.985	99.9049	0.148
3.927-4.16	0.219	70	0.156	906	0.16	976	0.97	0.985	100	0.15
4.16-4.44	0.185	38	0.15	910	0.151	948	0.975	0.986	100	0.149
4.44-4.785	0.235	51	0.154	815	0.158	867	0.961	0.986	99.8847	0.153
4.785-5.225	0.244	40	0.184	771	0.187	811	0.969	0.98	100	0.184
5.225-5.814	0.289	21	0.215	713	0.218	735	0.957	0.976	99.8639	0.215
5.814-6.663	0.239	36	0.226	608	0.227	650	0.966	0.971	99.0769	0.226
6.663-8.038	0.218	18	0.178	529	0.179	553	0.969	0.98	98.915	0.194
8.038-10.895	0.168	16	0.135	425	0.136	443	0.987	0.989	99.5485	0.159
10.895-26.985	0.178	12	0.183	261	0.183	290	0.967	0.978	94.1379	0.211

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