4DKD
Crystal Structure of Human Interleukin-34 Bound to Human CSF-1R
- PDB DOI: https://doi.org/10.2210/pdb4DKD/pdb
- Classification: CYTOKINE/TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2012-02-03 Released: 2012-04-11 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.287 
- R-Value Work: 0.252 
- R-Value Observed: 0.254 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Interleukin-34 | 185 | Homo sapiens | Mutation(s): 0  Gene Names: IL34, C16orf77 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q6ZMJ4 (Homo sapiens) Explore Q6ZMJ4  Go to UniProtKB:  Q6ZMJ4 | |||||
PHAROS:  Q6ZMJ4 GTEx:  ENSG00000157368  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6ZMJ4 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Macrophage colony-stimulating factor 1 receptor | 292 | Homo sapiens | Mutation(s): 0  Gene Names: CSF1R, FMS EC: 2.7.10.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P07333 (Homo sapiens) Explore P07333  Go to UniProtKB:  P07333 | |||||
PHAROS:  P07333 GTEx:  ENSG00000182578  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P07333 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | H [auth C], I [auth C], J [auth C], K [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
BMA Query on BMA | F [auth A], G [auth B] | beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.287 
- R-Value Work: 0.252 
- R-Value Observed: 0.254 
- Space Group: P 31 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 101.361 | α = 90 |
b = 101.361 | β = 90 |
c = 175.252 | γ = 120 |
Software Name | Purpose |
---|---|
Blu-Ice | data collection |
PHASES | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-04-11  Deposition Author(s): Ma, X., Bazan, J.F., Starovasnik, M.A.
Revision History (Full details and data files)
- Version 1.0: 2012-04-11
Type: Initial release - Version 1.1: 2012-04-25
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary