4R4N Viral Protein Immune System Inhibitor date Aug 19, 2014
title Crystal Structure Of The Anti-Hiv-1 Antibody 2.2c In Complex 93ug037 Gp120
authors P.Acharya, R.Louder, P.D.Kwong
compound source
Molecule: Hiv-1 Gp120
Chain: A, B, I, E, M, P, S, V
Engineered: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_common: Hiv-1
Organism_taxid: 11676
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: 293s

Molecule: M48u1 Peptide
Chain: a, b, e, I, m, p, s, v
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Antibody 2.2c Light Chain
Chain: L, D, G, K, O, R, U, X
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606

Molecule: Antibody 2.2c Heavy Chain
Chain: H, C, F, J, N, Q, T, W
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
symmetry Space Group: P 1
R_factor 0.296 R_Free 0.328
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.967 144.178 158.351 110.58 92.30 99.19
method X-Ray Diffractionresolution 3.56 Å
ligand DPR, MPT, NAG, NH2, OAS, U2X enzyme
Gene
Ontology
ChainFunctionProcessComponent
S, A, M, P, I, E, B, V


Primary referenceStructural Definition of an Antibody-Dependent Cellular Cytotoxicity (ADCC) Response Implicated in Reduced Risk for HIV-1 Infection., Acharya P, Tolbert WD, Gohain N, Wu X, Yu L, Liu T, Huang W, Huang CC, Do Kwon Y, Louder RK, Luongo TS, McLellan JS, Pancera M, Yang Y, Zhang B, Flinko R, Foulke JS Jr, Sajadi MM, Kamin-Lewis R, Robinson JE, Martin L, Kwong PD, Guan Y, DeVico AL, Lewis GK, Pazgier M, J Virol. 2014 Aug 27. pii: JVI.02194-14. PMID:25165110
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3113 Kb) [Save to disk]
  • Biological Unit Coordinates (4r4n.pdb1.gz) 401 Kb
  • Biological Unit Coordinates (4r4n.pdb2.gz) 404 Kb
  • Biological Unit Coordinates (4r4n.pdb3.gz) 404 Kb
  • Biological Unit Coordinates (4r4n.pdb4.gz) 398 Kb
  • Biological Unit Coordinates (4r4n.pdb5.gz) 405 Kb
  • Biological Unit Coordinates (4r4n.pdb6.gz) 404 Kb
  • Biological Unit Coordinates (4r4n.pdb7.gz) 403 Kb
  • Biological Unit Coordinates (4r4n.pdb8.gz) 405 Kb
  • LPC: Ligand-Protein Contacts for 4R4N
  • CSU: Contacts of Structural Units for 4R4N
  • Structure Factors (1744 Kb)
  • Retrieve 4R4N in mmCIF format [Save to disk]
  • Re-refined 4r4n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R4N 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 4R4N
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4R4N, from MSDmotif at EBI
  • Fold representative 4r4n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r4n_P] [4r4n_X] [4r4n_Q] [4r4n_s] [4r4n_A] [4r4n_a] [4r4n_e] [4r4n_I] [4r4n_E] [4r4n_F] [4r4n_i] [4r4n_V] [4r4n_m] [4r4n_T] [4r4n_v] [4r4n_U] [4r4n_D] [4r4n_K] [4r4n_b] [4r4n_L] [4r4n_S] [4r4n_J] [4r4n_O] [4r4n] [4r4n_p] [4r4n_R] [4r4n_M] [4r4n_C] [4r4n_W] [4r4n_N] [4r4n_B] [4r4n_H] [4r4n_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4R4N: [IG_like] [IGv ] by SMART
  • Other resources with information on 4R4N
  • Community annotation for 4R4N at PDBWiki (http://pdbwiki.org)

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