3KQ4

Structure of Intrinsic Factor-Cobalamin bound to its receptor Cubilin

PDB DOI: https://doi.org/10.2210/pdb3KQ4/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Komagataella pastoris, Cricetulus griseus
Mutation(s): No

Deposited: 2009-11-17 Released: 2010-03-09
Deposition Author(s): Andersen, C.B.F., Madsen, M., Moestrup, S.K., Andersen, G.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.242
R-Value Work: 0.211
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 299.19 kDa
Atom Count: 20,793
Modelled Residue Count: 2,526
Deposited Residue Count: 2,550
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gastric intrinsic factor	A, C, E	393	Homo sapiens	Mutation(s): 0 Gene Names: GIF, IFMH
UniProt & NIH Common Fund Data Resources
Find proteins for P27352 (Homo sapiens) Explore P27352 Go to UniProtKB: P27352
PHAROS: P27352 GTEx: ENSG00000134812
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27352
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cubilin	B, D, F	457	Homo sapiens	Mutation(s): 0 Gene Names: CUBN, IFCR
UniProt & NIH Common Fund Data Resources
Find proteins for O60494 (Homo sapiens) Explore O60494 Go to UniProtKB: O60494
PHAROS: O60494 GTEx: ENSG00000107611
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60494
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)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, J, K, M G, H, J, K, M, N	5		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain J Focus chain K Focus chain M Focus chain N Interactions & Density Focus chain G Focus chain H Focus chain J Focus chain K Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	I, L, O	2		N-Glycosylation	Interactions Focus chain I Focus chain L Focus chain O Interactions & Density Focus chain I Focus chain L Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 Query on B12 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain OA [auth E] SDF format, chain Q [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth A]	CA [auth C], OA [auth E], Q [auth A]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain CA [auth C] Focus chain OA [auth E] Focus chain Q [auth A] Interactions & Density Focus chain CA [auth C] Focus chain OA [auth E] Focus chain Q [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain NA [auth E] SDF format, chain P [auth A] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	BA [auth C] DA [auth D] EA [auth D] FA [auth D] GA [auth D] BA [auth C], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], IA [auth D], NA [auth E], P [auth A], PA [auth F], QA [auth F], R [auth B], RA [auth F], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain NA [auth E] Focus chain P [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain NA [auth E] Focus chain P [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain W [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain X [auth B] SDF format, chain XA [auth F] SDF format, chain Y [auth B] SDF format, chain YA [auth F] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth B]	AA [auth B] JA [auth D] KA [auth D] LA [auth D] MA [auth D] AA [auth B], JA [auth D], KA [auth D], LA [auth D], MA [auth D], VA [auth F], WA [auth F], X [auth B], XA [auth F], Y [auth B], YA [auth F], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.242
R-Value Work: 0.211
R-Value Observed: 0.211
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.684	α = 90
b = 204.179	β = 90
c = 410.023	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-10-24
Changes: Non-polymer description
Version 1.3: 2018-03-07
Changes: Advisory, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary