6CZP | pdb_00006czp

2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB from Vibrio vulnificus in Complex with FMN

PDB DOI: https://doi.org/10.2210/pdb6CZP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio vulnificus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-09 Released: 2018-04-25
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Grimshaw, S., Kwon, K., Savchenko, A., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.224 (Depositor), 0.230 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (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

2.2 Angstrom Resolution Crystal Structure Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB from Vibrio vulnificus in Complex with FMN.

Minasov, G., Wawrzak, Z., Skarina, T., Grimshaw, S., Kwon, K., Savchenko, A., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 200.66 kDa
Atom Count: 14,695
Modeled Residue Count: 1,746
Deposited Residue Count: 1,760
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen-insensitive NAD(P)H nitroreductase	A, B, C, D, E A, B, C, D, E, F, G, H	220	Vibrio vulnificus	Mutation(s): 0 Gene Names: FORC36_4330
UniProt
Find proteins for Q7MCD2 (Vibrio vulnificus (strain YJ016)) Explore Q7MCD2 Go to UniProtKB: Q7MCD2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MCD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain Z [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Z [auth H]	I [auth A] J [auth B] M [auth C] P [auth D] S [auth E] I [auth A], J [auth B], M [auth C], P [auth D], S [auth E], U [auth F], W [auth G], Z [auth H]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Z [auth H]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain O [auth C] SDF format, chain Y [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain O [auth C] MOL2 format, chain Y [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain O [auth C] mmCIF format, chain Y [auth G]	BA [auth H], O [auth C], Y [auth G]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain O [auth C] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain O [auth C] Focus chain Y [auth G]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain R [auth D] SDF format, chain V [auth F] MOL2 format, chain L [auth B] MOL2 format, chain R [auth D] MOL2 format, chain V [auth F] mmCIF format, chain L [auth B] mmCIF format, chain R [auth D] mmCIF format, chain V [auth F]	L [auth B], R [auth D], V [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain R [auth D] Focus chain V [auth F] Interactions & Density Focus chain L [auth B] Focus chain R [auth D] Focus chain V [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain K [auth B] SDF format, chain T [auth E] MOL2 format, chain AA [auth H] MOL2 format, chain K [auth B] MOL2 format, chain T [auth E] mmCIF format, chain AA [auth H] mmCIF format, chain K [auth B] mmCIF format, chain T [auth E]	AA [auth H], K [auth B], T [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain K [auth B] Focus chain T [auth E] Interactions & Density Focus chain AA [auth H] Focus chain K [auth B] Focus chain T [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain X [auth G] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain X [auth G] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain X [auth G]	N [auth C], Q [auth D], X [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth C] Focus chain Q [auth D] Focus chain X [auth G] Interactions & Density Focus chain N [auth C] Focus chain Q [auth D] Focus chain X [auth G]