6VMJ | pdb_00006vmj

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

• PDB DOI: https://doi.org/10.2210/pdb6VMJ/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2020-01-28 Released: 2021-02-03 
• Deposition Author(s): Wu, P., Harris, S.F., Eigenbrot, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.265 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

Dion, M., Wu, P., Morando, A., Bullen, G., Shatz, W., Harris, S.F., Eigenbrot, C., Loyet, K.M., Yadav, D., Tassew, N., Booler, H., Scheer, J., Kelley, R.F., Tesar, D.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 287.02 kDa 
• Atom Count: 19,932 
• Modeled Residue Count: 2,610 
• Deposited Residue Count: 2,660 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab20D12 Light Chain	A, C [auth E], E [auth I], G [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab20D12 heavy chain	B, D [auth F], F [auth J], H [auth M]	223	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement factor D	I [auth W], J [auth X], K [auth Y], L [auth Z]	228	Homo sapiens	Mutation(s): 0  Gene Names: CFD, DF, PFD EC: 3.4.21.46
UniProt & NIH Common Fund Data Resources
Find proteins for P00746 (Homo sapiens) Explore P00746  Go to UniProtKB:  P00746
PHAROS:  P00746 GTEx:  ENSG00000197766

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	M [auth B], N [auth F], O [auth J], P [auth M], Q [auth W], R [auth X]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.265 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.843	α = 90
b = 180.843	β = 90
c = 304.189	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Wu, P., Harris, S.F., Eigenbrot, C.

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary