3B2U

Crystal structure of isolated domain III of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8

PDB DOI: https://doi.org/10.2210/pdb3B2U/pdb

Classification: IMMUNE SYSTEM/TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda, Mus musculus
Mutation(s): No

Deposited: 2007-10-19 Released: 2008-02-19
Deposition Author(s): Ferguson, K.M., Li, S., Kussie, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.291
R-Value Work: 0.227
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 577.65 kDa
Atom Count: 39,035
Modelled Residue Count: 4,984
Deposited Residue Count: 5,200
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMC-11F8 Fab Light chain	A [auth L] D G J [auth K] M [auth O] A [auth L], D, G, J [auth K], M [auth O], P [auth R], S [auth U], V [auth X]	213	Homo sapiens	Mutation(s): 0 Gene Names: EGFR
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMC-11F8 Fab Heavy chain	B [auth H] E [auth C] H [auth F] K [auth J] N B [auth H], E [auth C], H [auth F], K [auth J], N, Q, T, W	223	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6GMX6 (Homo sapiens) Explore Q6GMX6 Go to UniProtKB: Q6GMX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6GMX6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	C [auth A] F [auth B] I [auth E] L [auth I] O [auth M] C [auth A], F [auth B], I [auth E], L [auth I], O [auth M], R [auth P], U [auth S], X [auth V]	214	Homo sapiens	Mutation(s): 0 Gene Names: EGFR, ERBB1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens) Explore P00533 Go to UniProtKB: P00533
PHAROS: P00533 GTEx: ENSG00000146648
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], EA [auth e], Y	4		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain EA [auth e] Focus chain Y Interactions & Density Focus chain CA [auth c] Focus chain EA [auth e] Focus chain Y
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], DA [auth d], GA [auth g], LA [auth l], NA [auth n], BA [auth b], DA [auth d], GA [auth g], LA [auth l], NA [auth n], PA [auth p], Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain PA [auth p] Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain PA [auth p] Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], FA [auth f], IA [auth i], JA [auth j], KA [auth k], AA [auth a], FA [auth f], IA [auth i], JA [auth j], KA [auth k], MA [auth m], OA [auth o]	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain OA [auth o] Interactions & Density Focus chain AA [auth a] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain OA [auth o]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h]	5		N-Glycosylation	Interactions Focus chain HA [auth h] Interactions & Density Focus chain HA [auth h]
Glycosylation Resources
GlyTouCan: G78750JU GlyCosmos: G78750JU GlyGen: G78750JU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CB [auth M] SDF format, chain EB [auth P] SDF format, chain JB [auth V] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain AB [auth I] SDF format, chain DB [auth P] SDF format, chain GB [auth S] SDF format, chain HB [auth S] SDF format, chain KB [auth V] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain WA [auth E] SDF format, chain XA [auth E] MOL2 format, chain CB [auth M] MOL2 format, chain EB [auth P] MOL2 format, chain JB [auth V] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain AB [auth I] MOL2 format, chain DB [auth P] MOL2 format, chain GB [auth S] MOL2 format, chain HB [auth S] MOL2 format, chain KB [auth V] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E]	AB [auth I] CB [auth M] DB [auth P] EB [auth P] GB [auth S] AB [auth I], CB [auth M], DB [auth P], EB [auth P], GB [auth S], HB [auth S], JB [auth V], KB [auth V], QA [auth A], RA [auth A], TA [auth B], UA [auth B], WA [auth E], XA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth I] Focus chain CB [auth M] Focus chain DB [auth P] Focus chain EB [auth P] Focus chain GB [auth S] Focus chain HB [auth S] Focus chain JB [auth V] Focus chain KB [auth V] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain WA [auth E] Focus chain XA [auth E] Interactions & Density Focus chain AB [auth I] Focus chain CB [auth M] Focus chain DB [auth P] Focus chain EB [auth P] Focus chain GB [auth S] Focus chain HB [auth S] Focus chain JB [auth V] Focus chain KB [auth V] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain WA [auth E] Focus chain XA [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BB [auth O] SDF format, chain YA [auth E] SDF format, chain ZA [auth K] SDF format, chain FB [auth U] SDF format, chain IB [auth X] SDF format, chain LB [auth V] SDF format, chain SA [auth A] SDF format, chain VA [auth G] MOL2 format, chain BB [auth O] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth K] MOL2 format, chain FB [auth U] MOL2 format, chain IB [auth X] MOL2 format, chain LB [auth V] MOL2 format, chain SA [auth A] MOL2 format, chain VA [auth G]	BB [auth O] FB [auth U] IB [auth X] LB [auth V] SA [auth A] BB [auth O], FB [auth U], IB [auth X], LB [auth V], SA [auth A], VA [auth G], YA [auth E], ZA [auth K]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BB [auth O] Focus chain FB [auth U] Focus chain IB [auth X] Focus chain LB [auth V] Focus chain SA [auth A] Focus chain VA [auth G] Focus chain YA [auth E] Focus chain ZA [auth K] Interactions & Density Focus chain BB [auth O] Focus chain FB [auth U] Focus chain IB [auth X] Focus chain LB [auth V] Focus chain SA [auth A] Focus chain VA [auth G] Focus chain YA [auth E] Focus chain ZA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.291
R-Value Work: 0.227
R-Value Observed: 0.230
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.373	α = 90
b = 139.122	β = 90.02
c = 175.325	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-02-19

Deposition Author(s):

Ferguson, K.M.

Li, S.

Kussie, P.

Revision History (Full details and data files)

Version 1.0: 2008-02-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary