2CYD | pdb_00002cyd

Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae

PDB DOI: https://doi.org/10.2210/pdb2CYD/pdb

Classification: HYDROLASE
Organism(s): Enterococcus hirae
Expression System: Enterococcus hirae
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2005-07-06 Released: 2006-06-27
Deposition Author(s): Murata, T., Yamato, I., Kakinuma, Y., Shirouzu, M., Walker, J.E., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae

Murata, T., Yamato, I., Kakinuma, Y., Shirouzu, M., Walker, J.E., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 175.96 kDa
Atom Count: 12,831
Modeled Residue Count: 1,560
Deposited Residue Count: 1,560
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATP synthase subunit K	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	156	Enterococcus hirae	Mutation(s): 0 EC: 3.6.3.14 Membrane Entity: Yes
UniProt
Find proteins for P43457 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore P43457 Go to UniProtKB: P43457
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43457
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LHG Query on LHG Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain IA [auth H] SDF format, chain L [auth A] SDF format, chain LA [auth I] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain PA [auth J] SDF format, chain OA [auth J] SDF format, chain MA [auth I] SDF format, chain M [auth A] SDF format, chain JA [auth H] SDF format, chain GA [auth G] SDF format, chain FA [auth G] SDF format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain IA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain PA [auth J] MOL2 format, chain OA [auth J] MOL2 format, chain MA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain IA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth I] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain PA [auth J] mmCIF format, chain OA [auth J] mmCIF format, chain MA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] CA [auth F] FA [auth G] GA [auth G] IA [auth H] BA [auth F], CA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], L [auth A], LA [auth I], M [auth A], MA [auth I], O [auth B], OA [auth J], P [auth B], PA [auth J], R [auth C], S [auth C], V [auth D], W [auth D], Y [auth E], Z [auth E]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain L [auth A] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth J] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain L [auth A] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth J] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E]
UMQ Query on UMQ Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain T [auth C] MOL2 format, chain DA [auth F] MOL2 format, chain T [auth C] mmCIF format, chain DA [auth F] mmCIF format, chain T [auth C]	DA [auth F], T [auth C]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain DA [auth F] Focus chain T [auth C] Interactions & Density Focus chain DA [auth F] Focus chain T [auth C]
LI Query on LI Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain HA [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth I] SDF format, chain Q [auth C] SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain NA [auth J] SDF format, chain N [auth B] SDF format, chain EA [auth G] MOL2 format, chain AA [auth F] MOL2 format, chain HA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain NA [auth J] MOL2 format, chain N [auth B] MOL2 format, chain EA [auth G] mmCIF format, chain AA [auth F] mmCIF format, chain HA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth I] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain NA [auth J] mmCIF format, chain N [auth B] mmCIF format, chain EA [auth G]	AA [auth F] EA [auth G] HA [auth H] K [auth A] KA [auth I] AA [auth F], EA [auth G], HA [auth H], K [auth A], KA [auth I], N [auth B], NA [auth J], Q [auth C], U [auth D], X [auth E]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain K [auth A] Focus chain KA [auth I] Focus chain N [auth B] Focus chain NA [auth J] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain K [auth A] Focus chain KA [auth I] Focus chain N [auth B] Focus chain NA [auth J] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.648	α = 90
b = 125.779	β = 90
c = 210.196	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-06-27

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-06-27
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2018-06-20
Changes: Data collection, Database references
Version 1.4: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Refinement description