3F9K	Viral Protein, Recombination	date	Nov 14, 2008
title	Two Domain Fragment Of Hiv-2 Integrase In Complex With Ledgf
authors	S.Hare, P.Cherepanov
compound		source
Molecule: Integrase Chain: A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h P, S, T; Fragment: N-Terminal And Catalytic Domains, Unp Residues 11 Engineered: Yes		Organism_scientific: Human Immunodeficiency Virus Type 2 Organism_common: Hiv-2 Organism_taxid: 11720 Gene: Gag-Pol Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Pc2 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pcdf-Hiv2-In(Ntd+Ccd)
Molecule: Pc4 And Sfrs1-Interacting Protein Chain: C, G, K, O, S, W, a, e, I, m, q, u Fragment: Ledgf, Integrase Binding Domain, Unp Residues 347 Synonym: Ledgf, Lens Epithelium-Derived Growth Factor, Transcriptional Coactivator P75p52, Dense Fine Speckles 70 Protein, Dfs 70, Cll-Associated Antigen Kw-7; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Psip1, Dfs70, Ledgf, Psip2 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Pc2 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pes-Ibd-3c7
symmetry	Space Group: P 21 21 21	R_factor 0.225 R_Free 0.234
crystal cell	length a length b length c angle alpha angle beta angle gamma 201.360 202.500 280.480 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.20 Å
ligand	MG, ZN	enzyme
note	3F9K is a representative structure
Gene Ontology	Chain Function Process Component F, N, d, Y, E, V, Z, Q, k, h, M, g, t, A, J, s, B, l, p, c, I, R, o, U
Primary reference	A novel co-crystal structure affords the design of gain-of-function lentiviral integrase mutants in the presence of modified PSIP1/LEDGF/p75., Hare S, Shun MC, Gupta SS, Valkov E, Engelman A, Cherepanov P, PLoS Pathog. 2009 Jan;5(1):e1000259. Epub 2009 Jan 9. PMID:19132083

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (931 Kb) [Save to disk] Biological Unit Coordinates (3f9k.pdb1.gz) 86 Kb Biological Unit Coordinates (3f9k.pdb2.gz) 87 Kb Biological Unit Coordinates (3f9k.pdb3.gz) 86 Kb Biological Unit Coordinates (3f9k.pdb4.gz) 87 Kb Biological Unit Coordinates (3f9k.pdb5.gz) 87 Kb Biological Unit Coordinates (3f9k.pdb6.gz) 87 Kb Biological Unit Coordinates (3f9k.pdb7.gz) 86 Kb Biological Unit Coordinates (3f9k.pdb8.gz) 87 Kb Biological Unit Coordinates (3f9k.pdb9.gz) 87 Kb LPC: Ligand-Protein Contacts for 3F9K CSU: Contacts of Structural Units for 3F9K Likely Quarternary Molecular Structure file(s) for 3F9K Structure Factors (1465 Kb) Retrieve 3F9K in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3F9K from S2C, [Save to disk] Re-refined 3f9k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3F9K 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 3F9K

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3F9K, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3f9k_S] [3f9k_c] [3f9k_e] [3f9k_Z] [3f9k_q] [3f9k_p] [3f9k_B] [3f9k_h] [3f9k_A] [3f9k_E] [3f9k_Q] [3f9k_g] [3f9k_U] [3f9k_O] [3f9k_i] [3f9k_I] [3f9k_t] [3f9k_s] [3f9k_F] [3f9k_k] [3f9k_C] [3f9k_W] [3f9k_K] [3f9k_m] [3f9k_R] [3f9k] [3f9k_N] [3f9k_o] [3f9k_l] [3f9k_a] [3f9k_u] [3f9k_Y] [3f9k_V] [3f9k_M] [3f9k_d] [3f9k_G] [3f9k_J] SWISS-PROT database: [P04584] [O75475] Domain organization of [POL_HV2RO] [PSIP1_HUMAN] by SWISSPFAM

Other resources with information on 3F9K

Community annotation for 3F9K at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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