13FC | pdb_000013fc

Polar Interface Homodimer - S3G

PDB DOI: https://doi.org/10.2210/pdb13FC/pdb

Classification: DE NOVO PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-05-04 Released: 2026-10-07
Deposition Author(s): Harvey, B.T., Kuhlman, B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.216 (Depositor), 0.224 (DCC)
R-Value Work:
0.168 (Depositor), 0.177 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 13FC

This is version 1.0 of the entry. See complete history.

Literature

Deep learning-based design of buried hydrogen bond networks with HBDesigner

Harvey, B.T., Dieckhaus, H., Mulikova, T., Horenstein, J., Nicely, N., Randolph, N.Z., Kuhlman, B.

To be published.

Macromolecule Content

Total Structure Weight: 23 kDa
Atom Count: 1,521
Modeled Residue Count: 184
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S3G	A, B	95	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.216 (Depositor), 0.224 (DCC)
R-Value Work: 0.168 (Depositor), 0.177 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.838	α = 90
b = 50.111	β = 90
c = 73.253	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM131923

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release