7DQD

Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase

PDB DOI: https://doi.org/10.2210/pdb7DQD/pdb

Classification: HYDROLASE
Organism(s): Enterococcus hirae ATCC 9790
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-12-23 Released: 2021-12-29
Deposition Author(s): Maruyama, S., Suzuki, K., Mizutani, K., Imai, F.L., Ishizuka-Katsura, Y., Shirouzu, M., Murata, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.38 Å
R-Value Free:
0.286 (Depositor), 0.290 (DCC)
R-Value Work:
0.261 (Depositor), 0.260 (DCC)
R-Value Observed:
0.262 (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

The combination of high-speed AFM and X-ray crystallography reveals rotary catalysis

Imamura, M., Maruyama, S., Nakamoto, K., Kawai, F., Akiyama, T., Mizutani, K., Suzuki, K., Shirouzu, M., Iino, R., Uchihashi, T., Ando, T., Murata, T.

To be published.

Macromolecule Content

Total Structure Weight: 710.66 kDa
Atom Count: 46,484
Modelled Residue Count: 6,177
Deposited Residue Count: 6,390
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase catalytic subunit A	A B C G [auth I] H [auth J] A, B, C, G [auth I], H [auth J], I [auth K]	600	Enterococcus hirae ATCC 9790	Mutation(s): 1 Gene Names: ntpA, EHR_08260 EC: 7.2.2.1
UniProt
Find proteins for Q08636 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore Q08636 Go to UniProtKB: Q08636
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08636
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase subunit B	D E F J [auth L] K [auth M] D, E, F, J [auth L], K [auth M], L [auth N]	465	Enterococcus hirae ATCC 9790	Mutation(s): 1 Gene Names: ntpB, EHR_08265
UniProt
Find proteins for Q08637 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore Q08637 Go to UniProtKB: Q08637
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08637
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain R [auth J] SDF format, chain T [auth K] SDF format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth J] MOL2 format, chain T [auth K] MOL2 format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth J] mmCIF format, chain T [auth K] mmCIF format, chain N [auth B]	N [auth B], P [auth C], R [auth J], T [auth K]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth J] Focus chain T [auth K] Interactions & Density Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth J] Focus chain T [auth K]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth J] SDF format, chain U [auth K] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth J] MOL2 format, chain U [auth K] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth J] mmCIF format, chain U [auth K]	O [auth B], Q [auth C], S [auth J], U [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth J] Focus chain U [auth K] Interactions & Density Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth J] Focus chain U [auth K]