6KHM | pdb_00006khm

Lipase (Open form)

PDB DOI: https://doi.org/10.2210/pdb6KHM/pdb

Classification: HYDROLASE
Organism(s): Cutibacterium acnes HL110PA4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-16 Released: 2020-07-22
Deposition Author(s): Kim, H.J., Kwon, A.R.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.256 (Depositor), 0.260 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Closed, blocked, and open states of lipase from type II Cutibacterium acnes

Kim, H.J., Lee, B.J., Kwon, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 899.28 kDa
Atom Count: 64,002
Modeled Residue Count: 8,053
Deposited Residue Count: 8,242
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, alpha/beta domain protein	A B C D E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W [auth X], X [auth Y], Y [auth W], Z	317	Cutibacterium acnes HL110PA4	Mutation(s): 0 Gene Names: HMPREF9578_02569

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DKO (Subject of Investigation/LOI) Query on DKO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain NA [auth N] SDF format, chain RA [auth R] MOL2 format, chain BA [auth B] MOL2 format, chain NA [auth N] MOL2 format, chain RA [auth R] mmCIF format, chain BA [auth B] mmCIF format, chain NA [auth N] mmCIF format, chain RA [auth R]	BA [auth B], NA [auth N], RA [auth R]	octane-1,1-diol C₈ H₁₈ O₂ QYPUTBKHHRIDGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain NA [auth N] Focus chain RA [auth R] Interactions & Density Focus chain BA [auth B] Focus chain NA [auth N] Focus chain RA [auth R]
DKL (Subject of Investigation/LOI) Query on DKL Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain CA [auth C] SDF format, chain QA [auth Q] SDF format, chain TA [auth T] SDF format, chain WA [auth X] MOL2 format, chain AA [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain QA [auth Q] MOL2 format, chain TA [auth T] MOL2 format, chain WA [auth X] mmCIF format, chain AA [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain QA [auth Q] mmCIF format, chain TA [auth T] mmCIF format, chain WA [auth X]	AA [auth A], CA [auth C], QA [auth Q], TA [auth T], WA [auth X]	heptane-1,1-diol C₇ H₁₆ O₂ MHIBEGOZTWERHF-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain CA [auth C] Focus chain QA [auth Q] Focus chain TA [auth T] Focus chain WA [auth X] Interactions & Density Focus chain AA [auth A] Focus chain CA [auth C] Focus chain QA [auth Q] Focus chain TA [auth T] Focus chain WA [auth X]
DKF (Subject of Investigation/LOI) Query on DKF Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain IA [auth I] SDF format, chain JA [auth J] SDF format, chain KA [auth K] SDF format, chain LA [auth L] SDF format, chain UA [auth U] SDF format, chain XA [auth Y] SDF format, chain YA [auth W] SDF format, chain VA [auth V] SDF format, chain MA [auth M] SDF format, chain GA [auth G] MOL2 format, chain EA [auth E] MOL2 format, chain IA [auth I] MOL2 format, chain JA [auth J] MOL2 format, chain KA [auth K] MOL2 format, chain LA [auth L] MOL2 format, chain UA [auth U] MOL2 format, chain XA [auth Y] MOL2 format, chain YA [auth W] MOL2 format, chain VA [auth V] MOL2 format, chain MA [auth M] MOL2 format, chain GA [auth G] mmCIF format, chain EA [auth E] mmCIF format, chain IA [auth I] mmCIF format, chain JA [auth J] mmCIF format, chain KA [auth K] mmCIF format, chain LA [auth L] mmCIF format, chain UA [auth U] mmCIF format, chain XA [auth Y] mmCIF format, chain YA [auth W] mmCIF format, chain VA [auth V] mmCIF format, chain MA [auth M] mmCIF format, chain GA [auth G]	EA [auth E] GA [auth G] IA [auth I] JA [auth J] KA [auth K] EA [auth E], GA [auth G], IA [auth I], JA [auth J], KA [auth K], LA [auth L], MA [auth M], UA [auth U], VA [auth V], XA [auth Y], YA [auth W]	hexane-1,1-diol C₆ H₁₄ O₂ ACCCMOQWYVYDOT-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain GA [auth G] Focus chain IA [auth I] Focus chain JA [auth J] Focus chain KA [auth K] Focus chain LA [auth L] Focus chain MA [auth M] Focus chain UA [auth U] Focus chain VA [auth V] Focus chain XA [auth Y] Focus chain YA [auth W] Interactions & Density Focus chain EA [auth E] Focus chain GA [auth G] Focus chain IA [auth I] Focus chain JA [auth J] Focus chain KA [auth K] Focus chain LA [auth L] Focus chain MA [auth M] Focus chain UA [auth U] Focus chain VA [auth V] Focus chain XA [auth Y] Focus chain YA [auth W]
DK9 (Subject of Investigation/LOI) Query on DK9 Download:Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain OA [auth O] SDF format, chain PA [auth P] MOL2 format, chain FA [auth F] MOL2 format, chain OA [auth O] MOL2 format, chain PA [auth P] mmCIF format, chain FA [auth F] mmCIF format, chain OA [auth O] mmCIF format, chain PA [auth P]	FA [auth F], OA [auth O], PA [auth P]	pentane-1,1-diol C₅ H₁₂ O₂ UWJJYHHHVWZFEP-UHFFFAOYSA-N		Interactions Focus chain FA [auth F] Focus chain OA [auth O] Focus chain PA [auth P] Interactions & Density Focus chain FA [auth F] Focus chain OA [auth O] Focus chain PA [auth P]
DK6 (Subject of Investigation/LOI) Query on DK6 Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain HA [auth H] SDF format, chain SA [auth S] SDF format, chain ZA [auth Z] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth H] MOL2 format, chain SA [auth S] MOL2 format, chain ZA [auth Z] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth H] mmCIF format, chain SA [auth S] mmCIF format, chain ZA [auth Z]	DA [auth D], HA [auth H], SA [auth S], ZA [auth Z]	propane-1,1-diol C₃ H₈ O₂ ULWHHBHJGPPBCO-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain HA [auth H] Focus chain SA [auth S] Focus chain ZA [auth Z] Interactions & Density Focus chain DA [auth D] Focus chain HA [auth H] Focus chain SA [auth S] Focus chain ZA [auth Z]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.256 (Depositor), 0.260 (DCC)
R-Value Work: 0.185 (Depositor), 0.194 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.857	α = 90
b = 185.857	β = 90
c = 205.099	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-22

Deposition Author(s):

Kim, H.J.

Kwon, A.R.

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	2017R1D1A1B03033857
National Research Foundation (Korea)	Korea, Republic Of	2018R1A5A2024425

Revision History (Full details and data files)

Version 1.0: 2020-07-22
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 2.0: 2025-09-17
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary