5MVZ | pdb_00005mvz

Fab 4AB007 bound to Interleukin-1-beta

• PDB DOI: https://doi.org/10.2210/pdb5MVZ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-01-17 Released: 2017-02-15 
• Deposition Author(s): Stark, W., Seibert, V.
• Funding Organization(s): KTI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Structure of a novel, fully Human Fab binding to Interleukin 1-beta.

Stark, W., Seibert, V.

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.

Macromolecule Content 

• Total Structure Weight: 147.64 kDa 
• Atom Count: 9,536 
• Modeled Residue Count: 1,151 
• Deposited Residue Count: 1,332 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 4AB007 H-chain	A [auth H], D [auth A]	240	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 4AB007 L-chain	B [auth L], E [auth B]	249	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta	C [auth U], F [auth V]	177	Homo sapiens	Mutation(s): 0  Gene Names: IL1B
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens) Explore P01584  Go to UniProtKB:  P01584
PHAROS:  P01584 GTEx:  ENSG00000125538

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth H], H [auth L], I [auth L], J [auth L], K [auth A], L [auth B], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.041	α = 90
b = 158.385	β = 90
c = 153.437	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Stark, W., Seibert, V.

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Funding Organization	Location	Grant Number
KTI	Switzerland	12972.1

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Structure summary