5F9W	Immune System	date	Dec 10, 2015
title	Crystal Structure Of Broadly Neutralizing Vh1-46 Germline-De Binding Site-Directed Antibody Ch235 In Complex With Hiv-1 93th057 Gp120
authors	L.Chen, T.Zhou, P.D.Kwong
compound		source
Molecule: Clade Ae 93th057 Hiv-1 Gp120 Core Chain: A, G Engineered: Yes		Organism_scientific: Human Immunodeficiency Virus 1 Organism_taxid: 11676 Gene: Hiv-1 Env Expression_system: Homo Sapiens Expression_system_taxid: 9606
Molecule: Heavy Chain Of Ch235-Lineage Antibody Ch235 Chain: B, H Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Homo Sapiens Expression_system_taxid: 9606
Molecule: Light Chain Of Ch235-Lineage Antibody Ch235 Chain: C, L Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Homo Sapiens Expression_system_taxid: 9606
symmetry	Space Group: P 32	R_factor 0.180 R_Free 0.232
crystal cell	length a length b length c angle alpha angle beta angle gamma 123.429 123.429 127.332 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.89 Å
ligand	NAG, PO4	enzyme
Gene Ontology	Chain Function Process Component A, G
Primary reference	Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody., Bonsignori M, Zhou T, Sheng Z, Chen L, Gao F, Joyce MG, Ozorowski G, Chuang GY, Schramm CA, Wiehe K, Alam SM, Bradley T, Gladden MA, Hwang KK, Iyengar S, Kumar A, Lu X, Luo K, Mangiapani MC, Parks RJ, Song H, Acharya P, Bailer RT, Cao A, Druz A, Georgiev IS, Kwon YD, Louder MK, Zhang B, Zheng A, Hill BJ, Kong R, Soto C, Mullikin JC, Douek DC, Montefiori DC, Moody MA, Shaw GM, Hahn BH, Kelsoe G, Hraber PT, Korber BT, Boyd SD, Fire AZ, Kepler TB, Shapiro L, Ward AB, Mascola JR, Liao HX, Kwong PD, Haynes BF, Cell. 2016 Apr 7;165(2):449-63. doi: 10.1016/j.cell.2016.02.022. Epub 2016 Mar 3. PMID:26949186

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (530 Kb) [Save to disk] Biological Unit Coordinates (5f9w.pdb1.gz) 261 Kb Biological Unit Coordinates (5f9w.pdb2.gz) 261 Kb LPC: Ligand-Protein Contacts for 5F9W CSU: Contacts of Structural Units for 5F9W Structure Factors (347 Kb) Retrieve 5F9W in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5F9W from S2C, [Save to disk] Re-refined 5f9w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5F9W 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 5F9W

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5f9w_L] [5f9w_C] [5f9w] [5f9w_G] [5f9w_A] [5f9w_H] [5f9w_B] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5F9W: [IG_like] [IGv ] by SMART

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