6VMK Hydrolase Immune System date Jan 28, 2020
title Crystal Structure Of Human Complement Factor D With Anti-Fac 20d12
authors P.Wu, S.F.Harris, C.Eigenbrot
compound source
Molecule: Complement Factor D
Chain: W, C, F, I, N, Q, T, X, a, d, g, j, m, p, s, v
Synonym: Adipsin,C3 Convertase Activator,Properdin Factor D
Ec: 3.4.21.46
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cfd, Df, Pfd
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029

Molecule: Fab Y49r Light Chain
Chain: L, A, D, G, J, O, R, U, Y, b, e, h, k, n, q, t
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Fab Y49r Heavy Chain
Chain: M, B, E, H, K, P, S, V, Z, c, f, I, l, o, r, u
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 2 2 2
R_factor 0.174 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
263.704 301.454 458.842 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.01 Å
ligand GOL, SO4 enzyme Hydrolase E.C.3.4.21.46 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3381 Kb) [Save to disk]
  • Biological Unit Coordinates (6vmk.pdb1.gz) 224 Kb
  • Biological Unit Coordinates (6vmk.pdb2.gz) 225 Kb
  • Biological Unit Coordinates (6vmk.pdb3.gz) 223 Kb
  • Biological Unit Coordinates (6vmk.pdb4.gz) 224 Kb
  • Biological Unit Coordinates (6vmk.pdb5.gz) 224 Kb
  • Biological Unit Coordinates (6vmk.pdb6.gz) 224 Kb
  • Biological Unit Coordinates (6vmk.pdb7.gz) 225 Kb
  • Biological Unit Coordinates (6vmk.pdb8.gz) 225 Kb
  • Biological Unit Coordinates (6vmk.pdb9.gz) 225 Kb
  • LPC: Ligand-Protein Contacts for 6VMK
  • CSU: Contacts of Structural Units for 6VMK
  • Structure Factors (11936 Kb)
  • Retrieve 6VMK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6VMK from S2C, [Save to disk]
  • View 6VMK 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 6VMK
  • 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
  • Fold representative 6vmk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6vmk_W] [6vmk_M] [6vmk_d] [6vmk_A] [6vmk_c] [6vmk_j] [6vmk_J] [6vmk_h] [6vmk_G] [6vmk_v] [6vmk_i] [6vmk_K] [6vmk_N] [6vmk_F] [6vmk_T] [6vmk_b] [6vmk_X] [6vmk_O] [6vmk_P] [6vmk_Z] [6vmk_e] [6vmk_o] [6vmk_U] [6vmk_k] [6vmk_Y] [6vmk_L] [6vmk_B] [6vmk_S] [6vmk_r] [6vmk_C] [6vmk_s] [6vmk_p] [6vmk_m] [6vmk_n] [6vmk_I] [6vmk_q] [6vmk_l] [6vmk_u] [6vmk_H] [6vmk_f] [6vmk_g] [6vmk_D] [6vmk_R] [6vmk_Q] [6vmk_a] [6vmk_V] [6vmk_E] [6vmk_t]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6VMK
  • Community annotation for 6VMK at PDBWiki (http://pdbwiki.org)

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