3RUL

New strategy to analyze structures of glycopeptide-target complexes

PDB DOI: https://doi.org/10.2210/pdb3RUL/pdb

Classification: Signaling Protein/Antibiotic
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-05 Released: 2012-06-06
Deposition Author(s): Economou, N.J., Nahoum, V., Weeks, S.D., Grasty, K.C., Loll, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.277
R-Value Work: 0.243
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 43.9 kDa
Atom Count: 3,060
Modelled Residue Count: 344
Deposited Residue Count: 344
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A, B, C, D	79	Homo sapiens	Mutation(s): 0 Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
PHAROS: P0CG48 GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dalbavancin	E, F, G, H	7	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M12 Query on M12 Download Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain Y [auth H] SDF format, chain S [auth F] SDF format, chain V [auth G] MOL2 format, chain P [auth E] MOL2 format, chain Y [auth H] MOL2 format, chain S [auth F] MOL2 format, chain V [auth G]	P [auth E], S [auth F], V [auth G], Y [auth H]	10-METHYLUNDECANOIC ACID C₁₂ H₂₄ O₂ QJRRBVNPIKYRQJ-UHFFFAOYSA-N		Interactions Focus chain P [auth E] Focus chain S [auth F] Focus chain V [auth G] Focus chain Y [auth H] Interactions & Density Focus chain P [auth E] Focus chain S [auth F] Focus chain V [auth G] Focus chain Y [auth H]
N1L Query on N1L Download Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain T [auth G] SDF format, chain W [auth H] SDF format, chain Q [auth F] MOL2 format, chain N [auth E] MOL2 format, chain T [auth G] MOL2 format, chain W [auth H] MOL2 format, chain Q [auth F]	N [auth E], Q [auth F], T [auth G], W [auth H]	2-amino-2-deoxy-beta-D-glucopyranuronic acid C₆ H₁₁ N O₆ CRIPFXSBMSGPKB-LVBGKUAWSA-N		Interactions Focus chain N [auth E] Focus chain Q [auth F] Focus chain T [auth G] Focus chain W [auth H] Interactions & Density Focus chain N [auth E] Focus chain Q [auth F] Focus chain T [auth G] Focus chain W [auth H]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain R [auth F] SDF format, chain X [auth H] SDF format, chain U [auth G] MOL2 format, chain O [auth E] MOL2 format, chain R [auth F] MOL2 format, chain X [auth H] MOL2 format, chain U [auth G]	O [auth E], R [auth F], U [auth G], X [auth H]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain O [auth E] Focus chain R [auth F] Focus chain U [auth G] Focus chain X [auth H] Interactions & Density Focus chain O [auth E] Focus chain R [auth F] Focus chain U [auth G] Focus chain X [auth H]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	I [auth A], J [auth A], K [auth B], L [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCS Query on CCS	A, B, C, D	L-PEPTIDE LINKING	C₅ H₉ N O₄ S		CYS
OMY Query on OMY	E, F, G, H	L-PEPTIDE LINKING	C₉ H₁₀ Cl N O₄		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.277
R-Value Work: 0.243
R-Value Observed: 0.244
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.3	α = 90
b = 86.25	β = 90
c = 107.19	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Polymer sequence, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2023-12-06
Changes: Data collection, Derived calculations

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Help and Resources

3RUL

New strategy to analyze structures of glycopeptide-target complexes

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2