3NI3 | pdb_00003ni3

54-Membered ring macrocyclic beta-sheet peptide

PDB DOI: https://doi.org/10.2210/pdb3NI3/pdb

Classification: UNKNOWN FUNCTION
Mutation(s): No

Deposited: 2010-06-15 Released: 2010-09-15
Deposition Author(s): Sawaya, M.R., Eisenberg, D., Nowick, J.S., Korman, T.P., Khakshoor, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free:
0.157 (Depositor), 0.170 (DCC)
R-Value Work:
0.150 (Depositor), 0.161 (DCC)
R-Value Observed:
0.150 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

X-ray crystallographic structure of an artificial beta-sheet dimer.

Khakshoor, O., Lin, A.J., Korman, T.P., Sawaya, M.R., Tsai, S.C., Eisenberg, D., Nowick, J.S.

(2010) J Am Chem Soc 132: 11622-11628

PubMed: 20669960 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja103438w
Primary Citation Related Structures:
3NI3

PubMed Abstract:
This paper describes the X-ray crystallographic structure of a designed cyclic beta-sheet peptide that forms a well-defined hydrogen-bonded dimer that mimics beta-sheet dimers formed by proteins. The 54-membered ring macrocyclic peptide (1a) contains molecular template and turn units that induce beta-sheet structure in a heptapeptide strand that forms the dimerization interface. The X-ray crystallographic structure reveals the structures of the two "Hao" amino acids that help template the beta-sheet structure and the two delta-linked ornithine turn units that link the Hao-containing template to the heptapeptide beta-strand. The Hao amino acids adopt a conformation that resembles a tripeptide in a beta-strand conformation, with one edge of the Hao unit presenting an alternating array of hydrogen-bond donor and acceptor groups in the same pattern as that of a tripeptide beta-strand. The delta-linked ornithines adopt a conformation that resembles a hydrogen-bonded beta-turn, in which the ornithine takes the place of the i+1 and i+2 residues. The dimers formed by macrocyclic beta-sheet 1a resemble the dimers of many proteins, such as defensin HNP-3, the lambda-Cro repressor, interleukin 8, and the ribonuclease H domain of HIV-1 reverse transcriptase. The dimers of 1a self-assemble in the solid state into a barrel-shaped trimer of dimers in which the three dimers are arranged in a triangular fashion. Molecular modeling in which one of the three dimers is removed and the remaining two dimers are aligned face-to-face provides a model of the dimers of dimers of closely related macrocyclic beta-sheet peptides that were observed in solution.

Organizational Affiliation

Department of Chemistry, University of California, Irvine, California 92697-2025, USA.

Macromolecule Content

Total Structure Weight: 22.38 kDa
Atom Count: 1,825
Modeled Residue Count: 144
Deposited Residue Count: 144
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
54-membered ring macrocyclic beta-sheet peptide	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	12	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain P [auth G] SDF format, chain Q [auth H] SDF format, chain R [auth K] SDF format, chain O [auth F] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth K] MOL2 format, chain O [auth F] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth H] mmCIF format, chain R [auth K] mmCIF format, chain O [auth F] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth B] O [auth F] P [auth G] Q [auth H] M [auth A], N [auth B], O [auth F], P [auth G], Q [auth H], R [auth K]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth K] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H] Focus chain R [auth K]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4BF Query on 4BF	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₉ H₁₀ Br N O₂		TYR
HAO Query on HAO	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PEPTIDE-LIKE	C₁₀ H₁₁ N₃ O₅		--
ORN Query on ORN	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₂ N₂ O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.157 (Depositor), 0.170 (DCC)
R-Value Work: 0.150 (Depositor), 0.161 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.045	α = 90
b = 64.194	β = 90
c = 64.247	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations