8AD0 | pdb_00008ad0

X-ray structure of Na+-NQR from Vibrio cholerae in different conformation at 3.1 A

PDB DOI: https://doi.org/10.2210/pdb8AD0/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Vibrio cholerae
Expression System: Vibrio cholerae
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2022-07-07 Released: 2023-07-12
Deposition Author(s): Fritz, G.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.288 (Depositor), 0.290 (DCC)
R-Value Work:
0.248 (Depositor), 0.250 (DCC)
R-Value Observed:
0.251 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

X-ray structure of Na+-NQR from Vibrio cholerae at 3.4 A resolution

Fritz, G.

(2023) Nat Struct Mol Biol

Macromolecule Content

Total Structure Weight: 218.47 kDa
Atom Count: 14,408
Modeled Residue Count: 1,839
Deposited Residue Count: 1,956
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit A	A	468	Vibrio cholerae	Mutation(s): 0 Gene Names: nqrA, ERS013165_00619, ERS013186_02081, ERS013199_02394, ERS013202_01882, ERS013206_02986, ERS013207_01957 EC: 7.2.1.1
UniProt
Find proteins for A5F5X1 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5X1 Go to UniProtKB: A5F5X1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5F5X1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit B	B	415	Vibrio cholerae	Mutation(s): 0 Gene Names: nqrB, D6U24_04465, ERS013186_02082, ERS013198_02508, ERS013199_02395, ERS013200_04117, ERS013202_01883, ERS013206_02987, ERS013207_01958, EYB64_17950... nqrB, D6U24_04465, ERS013186_02082, ERS013198_02508, ERS013199_02395, ERS013200_04117, ERS013202_01883, ERS013206_02987, ERS013207_01958, EYB64_17950, F0H40_10090, FLM02_04820, FLM12_12920, FXE67_12105, HPY07_02915 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5X0 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5X0 Go to UniProtKB: A5F5X0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5F5X0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit C	C	257	Vibrio cholerae	Mutation(s): 0 Gene Names: nqrC, BC353_01370, D6U24_04470, ERS013165_00616, ERS013186_02083, ERS013198_02507, ERS013199_02396, ERS013200_04118, ERS013201_01110, ERS013202_01884... nqrC, BC353_01370, D6U24_04470, ERS013165_00616, ERS013186_02083, ERS013198_02507, ERS013199_02396, ERS013200_04118, ERS013201_01110, ERS013202_01884, ERS013206_02988, ERS013207_01959, F0H40_10095, FLM02_04815, FLM12_12915 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5Y7 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5Y7 Go to UniProtKB: A5F5Y7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5F5Y7
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit D	D	210	Vibrio cholerae	Mutation(s): 0 Gene Names: nqrD, BC353_01365, D6U24_04475, ERS013165_00615, ERS013186_02084, ERS013198_02506, ERS013199_02397, ERS013200_04119, ERS013201_01111, ERS013202_01885... nqrD, BC353_01365, D6U24_04475, ERS013165_00615, ERS013186_02084, ERS013198_02506, ERS013199_02397, ERS013200_04119, ERS013201_01111, ERS013202_01885, ERS013206_02989, ERS013207_01960, EYB64_17940, F0315_08345, F0H40_10100, F0M16_14020, FLM02_04810, FLM12_12910, HPY07_02925 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5Y6 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5Y6 Go to UniProtKB: A5F5Y6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5F5Y6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit E	E	198	Vibrio cholerae	Mutation(s): 0 Gene Names: nqrE, BC353_01360, D6U24_04480, ERS013165_00614, ERS013186_02085, ERS013198_02505, ERS013199_02398, ERS013200_04120, ERS013201_01112, ERS013202_01886... nqrE, BC353_01360, D6U24_04480, ERS013165_00614, ERS013186_02085, ERS013198_02505, ERS013199_02398, ERS013200_04120, ERS013201_01112, ERS013202_01886, ERS013206_02990, ERS013207_01961, EYB64_17935, F0315_08350, F0H40_10105, F0M16_14025, FLM02_04805, FLM12_12905, HPY07_02930 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5Y5 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5Y5 Go to UniProtKB: A5F5Y5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5F5Y5
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit F	F	408	Vibrio cholerae	Mutation(s): 0 Gene Names: nqrF, D6U24_04485, ERS013198_02504, ERS013199_02399, ERS013201_01113, ERS013202_01887, ERS013206_02991, EYB64_17930, FLM12_12900 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5Y4 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5Y4 Go to UniProtKB: A5F5Y4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5F5Y4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain R [auth F] MOL2 format, chain R [auth F] mmCIF format, chain R [auth F]	R [auth F]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain R [auth F] Interactions & Density Focus chain R [auth F]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth D] SDF format, chain Q [auth E] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E]	I [auth B], O [auth D], Q [auth E]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain I [auth B] Focus chain O [auth D] Focus chain Q [auth E] Interactions & Density Focus chain I [auth B] Focus chain O [auth D] Focus chain Q [auth E]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain M [auth C] MOL2 format, chain G [auth B] MOL2 format, chain M [auth C] mmCIF format, chain G [auth B] mmCIF format, chain M [auth C]	G [auth B], M [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain G [auth B] Focus chain M [auth C] Interactions & Density Focus chain G [auth B] Focus chain M [auth C]
RBF Query on RBF Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	RIBOFLAVIN C₁₇ H₂₀ N₄ O₆ AUNGANRZJHBGPY-SCRDCRAPSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain S [auth F] MOL2 format, chain P [auth D] MOL2 format, chain S [auth F] mmCIF format, chain P [auth D] mmCIF format, chain S [auth F]	P [auth D], S [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Focus chain S [auth F] Interactions & Density Focus chain P [auth D] Focus chain S [auth F]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]