3L4B | pdb_00003l4b

Crystal Structure of an Octomeric Two-Subunit TrkA K+ Channel Ring Gating Assembly, TM1088A:TM1088B, from Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb3L4B/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-12-18 Released: 2010-02-16
Deposition Author(s): Deller, M.C., Johnson, H.A., Miller, M., Spraggon, G., Wilson, I.A., Lesley, S.A., Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free:
0.308 (Depositor), 0.288 (DCC)
R-Value Work:
0.259 (Depositor), 0.277 (DCC)
R-Value Observed:
0.261 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of an Octomeric Two-Subunit TrkA K+ Channel Ring Gating Assembly, TM1088A:TM1088B, from Thermotoga maritima

Deller, M.C., Johnson, H.A., Miller, M., Spraggon, G., Lesley, S.A.

To be published.

Macromolecule Content

Total Structure Weight: 161.86 kDa
Atom Count: 9,045
Modeled Residue Count: 1,361
Deposited Residue Count: 1,444
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TrkA K+ Channel protein TM1088A	A, B, E, F	143	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM1088
UniProt
Find proteins for D3KFX7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore D3KFX7 Go to UniProtKB: D3KFX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3KFX7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TrkA K+ Channel protein TM1088B	C, D, G, H	218	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM1088
UniProt
Find proteins for D3KFX8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore D3KFX8 Go to UniProtKB: D3KFX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3KFX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain L [auth E] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain M [auth F] MOL2 format, chain L [auth E] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain M [auth F] mmCIF format, chain L [auth E] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B], L [auth E], M [auth F]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth E] Focus chain M [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth E] Focus chain M [auth F]
UNX Query on UNX 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]	UNKNOWN ATOM OR ION X		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.45 Å
R-Value Free: 0.308 (Depositor), 0.288 (DCC)
R-Value Work: 0.259 (Depositor), 0.277 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.778	α = 90
b = 96.778	β = 90
c = 305.098	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2020-09-02
Changes: Derived calculations, Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description