4KRM

Nanobody/VHH domain 7D12 in complex with domain III of the extracellular region of EGFR, pH 3.5

PDB DOI: https://doi.org/10.2210/pdb4KRM/pdb

Classification: TRANSFERASE/IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): No

Deposited: 2013-05-16 Released: 2013-08-28
Deposition Author(s): Ferguson, K.M., Schmitz, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.244
R-Value Work: 0.208
R-Value Observed: 0.210

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: 237.52 kDa
Atom Count: 14,859
Modelled Residue Count: 1,922
Deposited Residue Count: 2,082
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A, C, E, G, I A, C, E, G, I, K	214	Homo sapiens	Mutation(s): 0 Gene Names: EGFR, ERBB, ERBB1, HER1 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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody/VHH domain 7D12	B, D, F, H, J B, D, F, H, J, L	133	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
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	M, N, P, Q, R M, N, P, Q, R, S	4		N-Glycosylation	Interactions Focus chain M Focus chain N Focus chain P Focus chain Q Focus chain R Focus chain S Interactions & Density Focus chain M Focus chain N Focus chain P Focus chain Q Focus chain R Focus chain S
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	2		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth K] SDF format, chain DA [auth K] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth C] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Y [auth G] SDF format, chain AA [auth I] SDF format, chain BA [auth I] SDF format, chain Z [auth G] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth K] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth C] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth G] MOL2 format, chain AA [auth I] MOL2 format, chain BA [auth I] MOL2 format, chain Z [auth G]	AA [auth I] BA [auth I] CA [auth K] DA [auth K] T [auth A] AA [auth I], BA [auth I], CA [auth K], DA [auth K], T [auth A], U [auth A], V [auth C], W [auth E], X [auth E], Y [auth G], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth I] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth C] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth I] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth C] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth G] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.244
R-Value Work: 0.208
R-Value Observed: 0.210
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.702	α = 90
b = 147.245	β = 90
c = 254.799	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-08-28

Deposition Author(s):

Ferguson, K.M.

Schmitz, K.R.

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
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: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4KRM

Nanobody/VHH domain 7D12 in complex with domain III of the extracellular region of EGFR, pH 3.5

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2