9CG1 | pdb_00009cg1

DUF512 protein from Clostridium sporogenes

PDB DOI: https://doi.org/10.2210/pdb9CG1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium sporogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-06-28 Released: 2025-03-05
Deposition Author(s): Wang, B., Radle, M.I., Peduzzi, O., Solinski, A., Knox, H.L., Cui, J., Maurya, R., Yennawar, N., Booker, S.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.198 (Depositor), 0.198 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

DUF512 protein from Clostridium sporogenes

Wang, B., Radle, M.I., Peduzzi, O., Solinski, A., Knox, H.L., Cui, J., Maurya, R., Yennawar, N., Booker, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 53.86 kDa
Atom Count: 4,359
Modelled Residue Count: 443
Deposited Residue Count: 443
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Radical SAM protein	A	443	Clostridium sporogenes	Mutation(s): 0 Gene Names: CGS26_13040, FDB81_14220
UniProt
Find proteins for A0AAE4Z2Q4 (Clostridium sporogenes) Explore A0AAE4Z2Q4 Go to UniProtKB: A0AAE4Z2Q4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AAE4Z2Q4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SA8 (Subject of Investigation/LOI) Query on SA8 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE C₁₅ H₂₃ N₇ O₅ JISVTSUBJCPLSV-TWBCTODHSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A]	G [auth A], I [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A]
BO3 Query on BO3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]