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 Diffraction	resolution	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] (3302 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

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: [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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