3F6K
Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin
- PDB DOI: https://doi.org/10.2210/pdb3F6K/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): Yes 
- Deposited: 2008-11-06 Released: 2008-12-30 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.229 
- R-Value Work: 0.204 
- R-Value Observed: 0.205 
wwPDB Validation   3D Report Full Report
This is version 3.1 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 |
Sortilin | 685 | Homo sapiens | Mutation(s): 1  Gene Names: SORT1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q99523 (Homo sapiens) Explore Q99523  Go to UniProtKB:  Q99523 | |||||
PHAROS:  Q99523 GTEx:  ENSG00000134243  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q99523 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Neurotensin | B [auth N] | 13 | N/A | Mutation(s): 0  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P30990 (Homo sapiens) Explore P30990  Go to UniProtKB:  P30990 | |||||
PHAROS:  P30990 GTEx:  ENSG00000133636  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P30990 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C [auth B] | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | D [auth C] | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PGE Query on PGE | E [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N | |||
GOL Query on GOL | F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PCA Query on PCA | B [auth N] | L-PEPTIDE LINKING | C5 H7 N O3 | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.229 
- R-Value Work: 0.204 
- R-Value Observed: 0.205 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 145.76 | α = 90 |
b = 74.53 | β = 131.87 |
c = 108.33 | γ = 90 |
Software Name | Purpose |
---|---|
XDS | data scaling |
SHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
Entry History 
Deposition Data
- Released Date: 2008-12-30  Deposition Author(s): Quistgaard, E.M., Madsen, P., Groftehauge, M.K., Nissen, P., Petersen, C.M., Thirup, S.
Revision History (Full details and data files)
- Version 1.0: 2008-12-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 2.0: 2019-12-25
Changes: Database references, Derived calculations, Polymer sequence - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2023-12-27
Changes: Data collection, Database references, Structure summary