OCA Atlas for 1LDK

1LDK

Ligase

date

Apr 08, 2002

title

Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin Liga

authors

N.Zheng, B.A.Schulman, L.Song, J.J.Miller, P.D.Jeffrey, P.Wang, C. D.M.Koepp, S.J.Elledge, M.Pagano, R.C.Conaway, J.W.Conaway, J.W. N.P.Pavletich

compound

source

Molecule: Cullin Homolog
Chain: A
Fragment: Residues 15-410
Synonym: Cul1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t1

Molecule: Cullin Homolog
Chain: B
Fragment: Residues 411-776
Synonym: Cul1
Engineered: Yes

Molecule: Ring-Box Protein 1
Chain: C
Synonym: Rbx1
Engineered: Yes

Molecule: Cyclin Acdk2-Associated Protein P19
Chain: D
Synonym: Skp1, Rna Polymerase II Elongation Factor-Like Pro Organ Of Corti Protein 2, Ocp-II Protein, Transcription Elo Factor B, Siii;
Engineered: Yes

Molecule: Skp2-Like Protein Type Gamma
Chain: E
Synonym: Skp2-Fbox
Engineered: Yes

symmetry

Space Group: P 21 21 2

R_factor

0.289

R_Free

0.331

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
219.378	50.529	158.610	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.10 Å

ligand

enzyme

note

1LDK (Molecule of the Month:pdb60)

Gene
Ontology

Chain	Function	Process	Component
A
B
C
D

Primary reference

Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex., Zheng N, Schulman BA, Song L, Miller JJ, Jeffrey PD, Wang P, Chu C, Koepp DM, Elledge SJ, Pagano M, Conaway RC, Conaway JW, Harper JW, Pavletich NP, Nature 2002 Apr 18;416(6882):703-9. PMID:11961546

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (170 Kb) [Save to disk]

Biological Unit Coordinates (1ldk.pdb1.gz) 161 Kb

Biological Unit Coordinates (1ldk.pdb2.gz) 318 Kb

LPC: Ligand-Protein Contacts for 1LDK

CSU: Contacts of Structural Units for 1LDK

Likely Quarternary Molecular Structure file(s) for 1LDK

Retrieve 1LDK in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1LDK from S2C, [Save to disk]

View 1LDK in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1LDK

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1LDK, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1ldka_, region A [Jmol] [rasmolscript] [script source]
- Domain d1ldkb2, region B:411-686 [Jmol] [rasmolscript] [script source]
- Domain d1ldkb1, region B:687-776 [Jmol] [rasmolscript] [script source]
- Domain d1ldkc_, region C [Jmol] [rasmolscript] [script source]
- Domain d1ldkd2, region D:2002-2062 [Jmol] [rasmolscript] [script source]
- Domain d1ldkd1, region D:2084-2140 [Jmol] [rasmolscript] [script source]
- Domain d1ldke1, region E:3109-3149 [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ldk_B] [1ldk_E] [1ldk_D] [1ldk] [1ldk_A] [1ldk_C]

SWISS-PROT database: [Q13616] [P62877] [P63208] [Q13309]

Domain organization of [CUL1_HUMAN] [RBX1_HUMAN] [SKP1_HUMAN] [SKP2_HUMAN] by SWISSPFAM

Domains found in 1LDK: [CULLIN] [Cullin_Nedd8] [FBOX] [RING] [Skp1 ] by SMART

Other resources with information on 1LDK

Community annotation for 1LDK at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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