3CBA | pdb_00003cba

Crystal structure of Lipopeptide Detergent (LPD-12) (Hexagonal)

PDB DOI: https://doi.org/10.2210/pdb3CBA/pdb

Classification: DE NOVO PROTEIN
Mutation(s): No

Deposited: 2008-02-21 Released: 2008-09-09
Deposition Author(s): Ho, D.N., Pomroy, N.C., Cuesta-Seijo, J.A., Prive, G.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.243 (Depositor), 0.210 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Packing and Twinning in Orthorhombic and Hexagonal Crystals of Lipopeptide Detergent (LPD-12)

Ho, D.N., Pomroy, N.C., Cuesta-Seijo, J.A., Prive, G.G.

To be published.

Macromolecule Content

Total Structure Weight: 41.64 kDa
Atom Count: 2,788
Modeled Residue Count: 324
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPD-12	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	27	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMU Query on DMU Download Ideal Coordinates CCD File SDF format, chain AA [auth K] SDF format, chain BA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth F] SDF format, chain T [auth G] SDF format, chain U [auth H] SDF format, chain V [auth I] SDF format, chain W [auth I] SDF format, chain X [auth J] SDF format, chain Y [auth J] SDF format, chain Z [auth J] MOL2 format, chain AA [auth K] MOL2 format, chain BA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth F] MOL2 format, chain T [auth G] MOL2 format, chain U [auth H] MOL2 format, chain V [auth I] MOL2 format, chain W [auth I] MOL2 format, chain X [auth J] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth J] mmCIF format, chain AA [auth K] mmCIF format, chain BA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth F] mmCIF format, chain T [auth G] mmCIF format, chain U [auth H] mmCIF format, chain V [auth I] mmCIF format, chain W [auth I] mmCIF format, chain X [auth J] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth J]	AA [auth K] BA [auth L] M [auth A] N [auth B] O [auth B] AA [auth K], BA [auth L], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth D], R [auth D], S [auth F], T [auth G], U [auth H], V [auth I], W [auth I], X [auth J], Y [auth J], Z [auth J]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth I] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth J] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth I] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth J] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.243 (Depositor), 0.210 (DCC)
R-Value Work: 0.184 (Depositor), 0.180 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.261	α = 90
b = 127.261	β = 90
c = 42.85	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary