1AMT

Crystal structure of alamethicin at 1.5 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb1AMT/pdb

Classification: ANTIBIOTIC
Organism(s): Trichoderma viride
Mutation(s): No

Deposited: 1987-12-08 Released: 1988-10-09
Deposition Author(s): Fox, R.O., Richards, F.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Observed: 0.155

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

A Voltage-Gated Ion Channel Model Inferred from the Crystal Structure of Alamethicin at 1.5-A Resolution.

Fox Jr, R.O., Richards, F.M.

(1982) Nature 300: 325

PubMed: 6292726 Search on PubMed
DOI: https://doi.org/10.1038/300325a0
Primary Citation of Related Structures:
1AMT

PubMed Abstract:
The crystal structure of alamethicin in nonaqueous solvent has been determined, and refined at 1.5-A resolution. The molecular conformation of the three crystallographically independent molecules is largely alpha-helical with a bend in the helix axis at an internal proline residue. The helix structure is highly amphipathic as most of the solvent-accessible polar atoms lie on a narrow strip of surface parallel to the helix axis. Molecular models for the voltage-gated ion channel, with n-fold symmetry and based on the molecular conformations observed in the crystal, are characterized by strong surface complementarity, a hydrophilic interior and a hydrophobic exterior. The channel structures are stabilized by a hydrated annulus of hydrogen-bonded glutamine residues which produce the greatest restriction in the channel diameter.

Macromolecule Content

Total Structure Weight: 6.34 kDa
Atom Count: 449
Modelled Residue Count: 63
Deposited Residue Count: 63
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALAMETHICIN F30	A, B, C	21	Trichoderma viride	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CCN Query on CCN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	ACETONITRILE C₂ H₃ N WEVYAHXRMPXWCK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B]
MOH Query on MOH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C]	E [auth A] G [auth B] H [auth B] I [auth B] J [auth B] E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], R [auth C]	METHANOL C H₄ O OKKJLVBELUTLKV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB Query on AIB	A, B, C	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
PHL Query on PHL	A, B, C	L-PEPTIDE LINKING	C₉ H₁₃ N O		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000163 Query on PRD_000163	A, B, C	Alamethicin	Peptaibol / Antibiotic		Interactions Focus chain A Focus chain B Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Observed: 0.155
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.33	α = 90
b = 29.62	β = 120.4
c = 23.2	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1988-10-09

Deposition Author(s):

Fox, R.O.

Richards, F.M.

Revision History (Full details and data files)

Version 1.0: 1988-10-09
Type: Initial release
Version 1.1: 2011-06-14
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-07-27
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
Version 1.4: 2012-12-12
Changes: Other
Version 1.5: 2017-11-01
Changes: Derived calculations, Other