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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Lima, C.D."

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Search Summary

This query matches 190 Structures.

Refinements

Structure Determination Methodology

experimental (190)

Scientific Name of Source Organism

	Homo sapiens (49)
	Schizosaccharomyces pombe 972h- (39)
	Escherichia coli (20)
	Saccharomyces cerevisiae (15)
	Saccharomyces cerevisiae S288C (10)
	Encephalitozoon cuniculi (7)
	Mycobacterium tuberculosis (7)
	synthetic construct (6)
	Bacillus subtilis (5)
	Schizosaccharomyces pombe (5)

More...

Taxonomy

	Eukaryota (127)
	Bacteria (54)
	other sequences (6)
	Duplodnaviria (5)
	Varidnaviria (2)
	Archaea (1)
	Riboviria (1)

Experimental Method

	X-RAY DIFFRACTION (149)
	ELECTRON MICROSCOPY (41)

Polymer Entity Type

	Protein (190)
	RNA (7)
	NA-hybrid (6)
	DNA (5)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (24)
	2.0 - 2.5 (64)
	2.5 - 3.0 (62)
	3.0 - 3.5 (25)
	3.5 - 4.0 (10)
	4.0 - 4.5 (2)

Release Date

	1995 - 1999 (15)
	2000 - 2004 (54)
	2005 - 2009 (41)
	2010 - 2014 (23)
	2015 - 2019 (16)
	2020 - 2024 (41)

Enzyme Classification Name

	Hydrolases (69)
	Transferases (85)
	Ligases (52)
	Oxidoreductases (12)
	Isomerases (9)
	Lyases (5)

Symmetry Type

	Asymmetric (134)
	Cyclic (49)
	Dihedral (15)

SCOP Classification

	Alpha and beta proteins (a+b) (70)
	Alpha and beta proteins (a/b) (36)
	Artifacts (23)
	All alpha proteins (15)
	All beta proteins (9)
	Multi-domain proteins (alpha and beta) (6)

AllSelected

1 to 25 of 190 Structures

Page 1 of 8

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1AV5 \| pdb_00001av5	Download File View File

PKCI-SUBSTRATE ANALOG

Lima, C.D., Klein, M.G., Hendrickson, W.A.

(1997) Science 278: 286-290

Released	1998-03-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN KINASE C INTERACTING PROTEIN (protein)
Unique Ligands	AP2

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1CY9 \| pdb_00001cy9	Download File View File

CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM

Feinberg, H., Lima, C., Mondragon, A.

(1999) Nat Struct Biol 6: 918-922

Released	2000-03-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli K-12
Macromolecule	DNA TOPOISOMERASE I (protein)

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1CYY \| pdb_00001cyy	Download File View File

CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM

Feinberg, H., Lima, C., Mondragon, A.

(1999) Nat Struct Biol 6: 918-922

Released	2000-03-08
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Escherichia coli K-12
Macromolecule	DNA TOPOISOMERASE I (protein)
Unique Ligands	ZN

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1D8H \| pdb_00001d8h	Download File View File

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.

Lima, C.D., Wang, L.K., Shuman, S.

(1999) Cell 99: 533-543

Released	1999-11-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	mRNA TRIPHOSPHATASE CET1 (protein)
Unique Ligands	MN, SO4

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1D8I \| pdb_00001d8i	Download File View File

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.

Lima, C.D., Wang, L.K., Shuman, S.

(1999) Cell 99: 533-543

Released	1999-11-29
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	MRNA TRIPHOSPHATASE CET1 (protein)
Unique Ligands	SO4

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1ECL \| pdb_00001ecl	Download File View File

AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I (RESIDUES 2-590 OF MATURE PROTEIN) CLONING ARTIFACT ADDS TWO RESIDUES TO THE AMINO-TERMINUS WHICH WERE NOT OBSERVED IN THE EXPERIMENTAL ELECTRON DENSITY (GLY-2, SER-1).

Lima, C.D., Wang, J.C., Mondragon, A.

(1994) Nature 367: 138-146

Released	1995-07-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	ESCHERICHIA COLI TOPOISOMERASE I (protein)

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1EUV \| pdb_00001euv	Download File View File

X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX WITH SMT3, THE YEAST ORTHOLOG OF SUMO.

Mossessova, E., Lima, C.D.

(2000) Mol Cell 5: 865-876

Released	2000-06-07
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	UBITQUTIN-LIKE PROTEIN SMT3 (protein) ULP1 PROTEASE (protein)

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1FIT \| pdb_00001fit	Download File View File

FHIT (FRAGILE HISTIDINE TRIAD PROTEIN)

Lima, C.D., D'Amico, K.L., Naday, I., Rosenbaum, G., Westbrook, E.M., Hendrickson, W.A.

(1997) Structure 5: 763-774

Released	1997-11-19
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	FRAGILE HISTIDINE PROTEIN (protein)
Unique Ligands	FRU, SO4

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1JF9 \| pdb_00001jf9	Download File View File

Crystal Structure of selenocysteine lyase

Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

(2002) J Mol Biology 315: 1199-1208

Released	2001-07-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	SELENOCYSTEINE LYASE (protein)
Unique Ligands	PLP

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1JR7 \| pdb_00001jr7	Download File View File

CRYSTAL STRUCTURE OF GAB REVEALS OXIDOREDUCTASE FOLD

Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

(2002) Protein Sci 11: 723-738

Released	2001-08-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	HYPOTHETICAL 37.4 KDA PROTEIN IN ILEY-GABD INTERGENIC REGION (protein)
Unique Ligands	FE2

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1KMJ \| pdb_00001kmj	Download File View File

E. coli NifS/CsdB protein at 2.0A with the cysteine persulfide intermediate (residue CSS).

Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

(2002) J Mol Biology 315: 1199-1208

Released	2001-12-21
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	Selenocysteine lyase (protein)
Unique Ligands	PLP

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1KMK \| pdb_00001kmk	Download File View File

E. coli NifS/CsdB protein at 2.20A with the cysteine perselenide intermediate (residue CSZ).

Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

(2002) J Mol Biology 315: 1199-1208

Released	2001-12-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	SELENOCYSTEINE LYASE (protein)
Unique Ligands	PLP, SEC

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1KNC \| pdb_00001knc	Download File View File

Structure of AhpD from Mycobacterium tuberculosis, a novel enzyme with thioredoxin-like activity.

Bryk, R., Lima, C.D., Erdjument-Bromage, H., Tempst, P., Nathan, C.

(2002) Science 295: 1073-1077

Released	2002-01-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	AhpD protein (protein)
Unique Ligands	SO4

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1KPA \| pdb_00001kpa	Download File View File

PKCI-1-ZINC

Lima, C.D., Klein, M.G., Weinstein, I.B., Hendrickson, W.A.

(1996) Proc Natl Acad Sci U S A 93: 5357-5362

Released	1996-07-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	HUMAN PROTEIN KINASE C INTERACTING PROTEIN 1 (ZINC PROTEIN) (protein)

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1KPB \| pdb_00001kpb	Download File View File

PKCI-1-APO

Lima, C.D., Klein, M.G., Weinstein, I.B., Hendrickson, W.A.

(1996) Proc Natl Acad Sci U S A 93: 5357-5362

Released	1996-07-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	HUMAN PROTEIN KINASE C INTERACTING PROTEIN 1 (ZINC PROTEIN) (protein)

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1KPC \| pdb_00001kpc	Download File View File

PKCI-1-APO+ZINC

Lima, C.D., Klein, M.G., Weinstein, I.B., Hendrickson, W.A.

(1996) Proc Natl Acad Sci U S A 93: 5357-5362

Released	1996-07-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	HUMAN PROTEIN KINASE C INTERACTING PROTEIN 1 (ZINC PROTEIN) (protein)

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1KPE \| pdb_00001kpe	Download File View File

PKCI-TRANSITION STATE ANALOG

Lima, C.D., Klein, M.G., Hendrickson, W.A.

(1997) Science 278: 286-290

Released	1998-03-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN KINASE C INTERACTING PROTEIN (protein)
Unique Ligands	ADW

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1KPF \| pdb_00001kpf	Download File View File

PKCI-SUBSTRATE ANALOG

Lima, C.D., Klein, M.G., Hendrickson, W.A.

(1997) Science 278: 286-290

Released	1998-03-25
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN KINASE C INTERACTING PROTEIN (protein)
Unique Ligands	AMP

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1KPS \| pdb_00001kps	Download File View File

Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1

Bernier-Villamor, V., Sampson, D.A., Matunis, M.J., Lima, C.D.

(2002) Cell 108: 345-356

Released	2002-02-13
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Ran-GTPase activating protein 1 (protein) Ubiquitin-like protein SUMO-1 conjugating enzyme (protein)
Unique Ligands	SO4

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1LA2 \| pdb_00001la2	Download File View File

Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase

Kniewel, R., Buglino, J.A., Shen, V., Chadna, T., Beckwith, A., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

(2002) J Struct Funct Genomics 2: 129-134

Released	2002-04-10
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Myo-inositol-1-phosphate synthase (protein)
Unique Ligands	NAD

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1LNZ \| pdb_00001lnz	Download File View File

Structure of the Obg GTP-binding protein

Buglino, J., Shen, V., Hakimian, P., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

(2002) Structure 10: 1581-1592

Released	2002-09-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bacillus subtilis
Macromolecule	SPO0B-associated GTP-binding protein (protein)
Unique Ligands	G4P, MG

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1LX7 \| pdb_00001lx7	Download File View File

Structure of E. coli uridine phosphorylase at 2.0A

Burling, T., Buglino, J.A., Kniewel, R., Chadna, T., Beckwith, A., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

(2003) Acta Crystallogr D Biol Crystallogr 59: 73-76

Released	2002-06-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	uridine phosphorylase (protein)

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1LY1 \| pdb_00001ly1	Download File View File

Structure and Mechanism of T4 Polynucleotide Kinase

Wang, L.K., Lima, C.D., Shuman, S.

(2002) EMBO J 21: 3873-3880

Released	2002-07-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Tequatrovirus T4
Macromolecule	polynucleotide kinase (protein)
Unique Ligands	SO4

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1MW8 \| pdb_00001mw8	Download File View File

Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3'

Perry, K., Mondragon, A.

(2003) Structure 11: 1349-1358

Released	2003-10-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	DNA Topoisomerase I (protein) 5'-D(APCPTPTPCPGPGPGPAPTP*G)-3' (nucleic acid)
Unique Ligands	SO4, TMP