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

Find similar proteins by:

(by identity cutoff) | 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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 RA [auth R] SDF format, chain NA [auth N] SDF format, chain BA [auth B] MOL2 format, chain RA [auth R] MOL2 format, chain NA [auth N] MOL2 format, chain BA [auth B] mmCIF format, chain RA [auth R] mmCIF format, chain NA [auth N] mmCIF format, chain BA [auth B]	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 WA [auth X] SDF format, chain TA [auth T] SDF format, chain QA [auth Q] SDF format, chain CA [auth C] SDF format, chain AA [auth A] MOL2 format, chain WA [auth X] MOL2 format, chain TA [auth T] MOL2 format, chain QA [auth Q] MOL2 format, chain CA [auth C] MOL2 format, chain AA [auth A] mmCIF format, chain WA [auth X] mmCIF format, chain TA [auth T] mmCIF format, chain QA [auth Q] mmCIF format, chain CA [auth C] mmCIF format, chain AA [auth A]	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 YA [auth W] SDF format, chain XA [auth Y] SDF format, chain VA [auth V] SDF format, chain UA [auth U] SDF format, chain MA [auth M] SDF format, chain LA [auth L] SDF format, chain KA [auth K] SDF format, chain JA [auth J] SDF format, chain IA [auth I] SDF format, chain GA [auth G] SDF format, chain EA [auth E] MOL2 format, chain YA [auth W] MOL2 format, chain XA [auth Y] MOL2 format, chain VA [auth V] MOL2 format, chain UA [auth U] MOL2 format, chain MA [auth M] MOL2 format, chain LA [auth L] MOL2 format, chain KA [auth K] MOL2 format, chain JA [auth J] MOL2 format, chain IA [auth I] MOL2 format, chain GA [auth G] MOL2 format, chain EA [auth E] mmCIF format, chain YA [auth W] mmCIF format, chain XA [auth Y] mmCIF format, chain VA [auth V] mmCIF format, chain UA [auth U] mmCIF format, chain MA [auth M] mmCIF format, chain LA [auth L] mmCIF format, chain KA [auth K] mmCIF format, chain JA [auth J] mmCIF format, chain IA [auth I] mmCIF format, chain GA [auth G] mmCIF format, chain EA [auth E]	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 PA [auth P] SDF format, chain OA [auth O] SDF format, chain FA [auth F] MOL2 format, chain PA [auth P] MOL2 format, chain OA [auth O] MOL2 format, chain FA [auth F] mmCIF format, chain PA [auth P] mmCIF format, chain OA [auth O] mmCIF format, chain FA [auth F]	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 ZA [auth Z] SDF format, chain SA [auth S] SDF format, chain HA [auth H] SDF format, chain DA [auth D] MOL2 format, chain ZA [auth Z] MOL2 format, chain SA [auth S] MOL2 format, chain HA [auth H] MOL2 format, chain DA [auth D] mmCIF format, chain ZA [auth Z] mmCIF format, chain SA [auth S] mmCIF format, chain HA [auth H] mmCIF format, chain DA [auth D]	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

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