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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Miranda, M."

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Search Summary

This query matches 17 Structures.

Refinements

Structure Determination Methodology

experimental (17)

Scientific Name of Source Organism

	synthetic construct (15)
	Homo sapiens (2)
	Thermotoga maritima (1)

Taxonomy

	other sequences (15)
	Eukaryota (2)
	Bacteria (1)

Experimental Method

	X-RAY DIFFRACTION (12)
	ELECTRON MICROSCOPY (5)

Polymer Entity Type

Protein (17)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (1)
	2.5 - 3.0 (4)
	3.0 - 3.5 (1)
	3.5 - 4.0 (5)
	4.0 - 4.5 (4)
	> 4.5 (1)

Release Date

	2010 - 2014 (2)
	2020 - 2024 (15)

Enzyme Classification Name

Transferases (2)

Symmetry Type

	Asymmetric (11)
	Cyclic (6)
	Octahedral (1)
	Tetrahedral (1)

SCOP Classification

Alpha and beta proteins (a/b) (2)

AllSelected

1 to 17 of 17 Structures

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Explore in 3D

3IPX \| pdb_00003ipx	Download File View File

X-Ray structure of Human Deoxycytidine Kinase in complex with ADP and an inhibitor

Tari, L.W., Swanson, R.V., Hunter, M., Hoffman, I., Stouch, T.R., Carson, K.G.

(2009) Bioorg Med Chem Lett 19: 6784-6787

Released	2010-08-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Deoxycytidine kinase (protein)
Unique Ligands	ADP, B86, MG

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3IPY \| pdb_00003ipy	Download File View File

X-Ray structure of Human Deoxycytidine Kinase in complex with an inhibitor

Tari, L.W., Swanson, R.V., Hunter, M., Hoffman, I., Stouch, T.R., Carson, K.G.

(2009) Bioorg Med Chem Lett 19: 6784-6787

Released	2010-08-18
Method	X-RAY DIFFRACTION 2.54 Å
Organisms	Homo sapiens
Macromolecule	Deoxycytidine kinase (protein)
Unique Ligands	B87, MLT

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8CUS \| pdb_00008cus	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Li, Z., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 3.98 Å
Organisms	synthetic construct
Macromolecule	I432-1(NaCl) Chain A (protein) I432-1(NaCl) Chain B (protein)

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8CUT \| pdb_00008cut	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Li, Z., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 4 Å
Organisms	synthetic construct
Macromolecule	I432-1(Imd) Chain A (protein) I432-1(Imd) Chain B (protein)

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8CUU \| pdb_00008cuu	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Li, Z., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 2.91 Å
Organisms	synthetic construct
Macromolecule	F4132-1-0 chain A (protein) F4132-1-0 chain B (protein)

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8CUV \| pdb_00008cuv	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Li, Z., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	synthetic construct
Macromolecule	F4132-1 chain A (protein) F4132-1 chain B (protein)

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8CUW \| pdb_00008cuw	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Li, Z., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 3.55 Å
Organisms	synthetic construct
Macromolecule	F4132-1-3 Chain A (protein) F4132-1-3 Chain B (protein)

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8CUX \| pdb_00008cux	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Natterman, U., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	synthetic construct
Macromolecule	R3-1 Chain B (protein)

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8CWS \| pdb_00008cws	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Li, Z., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 4.4 Å
Organisms	synthetic construct
Macromolecule	F4132-2 Chain A (protein) F4132-2 Chain B (protein)

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8CWY \| pdb_00008cwy	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Li, Z., Borst, A.J., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	ELECTRON MICROSCOPY 3.34 Å
Organisms	synthetic construct
Macromolecule	T32-15-1 (protein) T32-15-2 (protein)

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8CWZ \| pdb_00008cwz	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Li, Z., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 5.53 Å
Organisms	synthetic construct
Macromolecule	I432-1-X3 Chain A (protein) I432-1-X3 Chain B (protein)

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8E1E \| pdb_00008e1e	Download File View File

Scaffolding protein functional sites using deep learning

Bera, A.K., Gerben, S., Baker, D.

(2023) Biochemistry 62: 358-368

Released	2023-08-16
Method	X-RAY DIFFRACTION 4.27 Å
Organisms	synthetic construct
Macromolecule	SG122_C3 (protein)

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8E55 \| pdb_00008e55	Download File View File

Design of Diverse Asymmetric Pockets in de novo Homo-oligomeric Proteins

Gerben, S., Borst, A.J., Baker, D.

(2023) Biochemistry 62: 358-368

Released	2023-01-25
Method	ELECTRON MICROSCOPY 3.85 Å
Organisms	synthetic construct
Macromolecule	SG135 (protein)

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8F6Q \| pdb_00008f6q	Download File View File

CryoEM structure of designed modular protein oligomer C8-71

Redler, R.L., Edman, N.I., Baker, D., Ekiert, D., Bhabha, G.

(2024) Cell 187: 3726-3740.e43

Released	2023-11-29
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	synthetic construct
Macromolecule	C8-71 (protein)

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8F6R \| pdb_00008f6r	Download File View File

CryoEM structure of designed modular protein oligomer C6-79

Redler, R.L., Edman, N.I., Baker, D., Ekiert, D., Bhabha, G.

(2024) Cell 187: 3726-3740.e43

Released	2023-11-29
Method	ELECTRON MICROSCOPY 4 Å
Organisms	synthetic construct
Macromolecule	De novo designed oligomeric protein C6-79 (protein)

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8FAR \| pdb_00008far	Download File View File

Accurate computational design of genetically encoded 3D protein crystals

Bera, A.K., Li, Z., Baker, D.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	X-RAY DIFFRACTION 3.66 Å
Organisms	synthetic construct
Macromolecule	I432-1-CC (protein)

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8SZZ \| pdb_00008szz	Download File View File

CryoEM Structure of Computationally Designed Nanocage O32-ZL4

Weidle, C., Borst, A.

(2023) Nat Mater 22: 1556-1563

Released	2023-11-01
Method	ELECTRON MICROSCOPY 2.9 Å
Organisms	Thermotoga maritima synthetic construct
Macromolecule	O32-ZL4 Component A (protein) O32-ZL4 Component B (protein)
Unique Ligands	NA

1 to 17 of 17 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

3IPX | pdb_00003ipx

X-Ray structure of Human Deoxycytidine Kinase in complex with ADP and an inhibitor

3IPY | pdb_00003ipy

X-Ray structure of Human Deoxycytidine Kinase in complex with an inhibitor

8CUS | pdb_00008cus

Accurate computational design of genetically encoded 3D protein crystals

8CUT | pdb_00008cut

Accurate computational design of genetically encoded 3D protein crystals

8CUU | pdb_00008cuu

Accurate computational design of genetically encoded 3D protein crystals

8CUV | pdb_00008cuv

Accurate computational design of genetically encoded 3D protein crystals

8CUW | pdb_00008cuw

Accurate computational design of genetically encoded 3D protein crystals

8CUX | pdb_00008cux

Accurate computational design of genetically encoded 3D protein crystals

8CWS | pdb_00008cws

Accurate computational design of genetically encoded 3D protein crystals

8CWY | pdb_00008cwy

Accurate computational design of genetically encoded 3D protein crystals

8CWZ | pdb_00008cwz

Accurate computational design of genetically encoded 3D protein crystals

8E1E | pdb_00008e1e

Scaffolding protein functional sites using deep learning

8E55 | pdb_00008e55

Design of Diverse Asymmetric Pockets in de novo Homo-oligomeric Proteins

8F6Q | pdb_00008f6q

CryoEM structure of designed modular protein oligomer C8-71

8F6R | pdb_00008f6r

CryoEM structure of designed modular protein oligomer C6-79

8FAR | pdb_00008far

Accurate computational design of genetically encoded 3D protein crystals

8SZZ | pdb_00008szz

CryoEM Structure of Computationally Designed Nanocage O32-ZL4

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

3IPX | pdb_00003ipx

3IPY | pdb_00003ipy

8CUS | pdb_00008cus

8CUT | pdb_00008cut

8CUU | pdb_00008cuu

8CUV | pdb_00008cuv

8CUW | pdb_00008cuw

8CUX | pdb_00008cux

8CWS | pdb_00008cws

8CWY | pdb_00008cwy

8CWZ | pdb_00008cwz

8E1E | pdb_00008e1e

8E55 | pdb_00008e55

8F6Q | pdb_00008f6q

8F6R | pdb_00008f6r

8FAR | pdb_00008far

8SZZ | pdb_00008szz