7CB8 | pdb_00007cb8

Structure of a FIC-domain protein from Mycobacterium marinum in complex with CDP

PDB DOI: https://doi.org/10.2210/pdb7CB8/pdb

Classification: TOXIN
Organism(s): Mycobacterium marinum M
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-11 Released: 2021-08-18
Deposition Author(s): Kumar, S., Singh, A., Penmatsa, A., Surolia, A.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.195 (Depositor), 0.190 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of of a FIC-domain protein from Mycobacterium marinum

Kumar, S., Singh, A., Penmatsa, A., Surolia, A.

To be published.

Macromolecule Content

Total Structure Weight: 92.73 kDa
Atom Count: 6,280
Modeled Residue Count: 787
Deposited Residue Count: 824
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fic-domain containing protein	A, B	412	Mycobacterium marinum M	Mutation(s): 0 Gene Names: MMAR_0586
UniProt
Find proteins for B2HP08 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HP08 Go to UniProtKB: B2HP08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2HP08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDP (Subject of Investigation/LOI) Query on CDP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B]	C [auth A], L [auth B]	CYTIDINE-5'-DIPHOSPHATE C₉ H₁₅ N₃ O₁₁ P₂ ZWIADYZPOWUWEW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	H [auth A], R [auth B], S [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] M [auth B] D [auth A], E [auth A], F [auth A], G [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	I [auth A], J [auth A], K [auth A], T [auth B], U [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B]