3NVQ
Molecular mechanism of guidance cue recognition
- PDB DOI: https://doi.org/10.2210/pdb3NVQ/pdb
- Classification: SIGNALING PROTEIN/protein binding
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2010-07-08 Released: 2010-09-15 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.277 
- R-Value Work: 0.248 
- R-Value Observed: 0.248 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Semaphorin-7A | A, C [auth E] | 590 | Homo sapiens | Mutation(s): 0  Gene Names: SEMA7A, CD108, SEMAL | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O75326 (Homo sapiens) Explore O75326  Go to UniProtKB:  O75326 | |||||
PHAROS:  O75326 GTEx:  ENSG00000138623  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O75326 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Plexin-C1 | B, D [auth F] | 476 | Homo sapiens | Mutation(s): 0  Gene Names: PLXNC1, VESPR | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O60486 (Homo sapiens) Explore O60486  Go to UniProtKB:  O60486 | |||||
PHAROS:  O60486 GTEx:  ENSG00000136040  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O60486 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NDG Query on NDG | H [auth A] | 2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N | |||
NAG Query on NAG | E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.277 
- R-Value Work: 0.248 
- R-Value Observed: 0.248 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 99.645 | α = 90 |
b = 126.078 | β = 90 |
c = 236.419 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
SOLVE | phasing |
RESOLVE | model building |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
RESOLVE | phasing |
Entry History 
Deposition Data
Revision History (Full details and data files)
- Version 1.0: 2010-09-15
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary