1YAJ

Crystal Structure of Human Liver Carboxylesterase in complex with benzil

PDB DOI: https://doi.org/10.2210/pdb1YAJ/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2004-12-17 Released: 2005-08-02
Deposition Author(s): Fleming, C.D., Bencharit, S., Edwards, C.C., Hyatt, J.L., Morton, C.M., Howard-Williams, E.L., Potter, P.M., Redinbo, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.287
R-Value Work: 0.207
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 715.67 kDa
Atom Count: 50,793
Modelled Residue Count: 6,384
Deposited Residue Count: 6,384
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CES1 protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	532	Homo sapiens	Mutation(s): 0 EC: 3.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P23141 (Homo sapiens) Explore P23141 Go to UniProtKB: P23141
PHAROS: P23141 GTEx: ENSG00000198848
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23141
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain CC [auth L] SDF format, chain DB [auth H] SDF format, chain FA [auth D] SDF format, chain LA [auth E] SDF format, chain WB [auth K] SDF format, chain JB [auth I] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain PB [auth J] SDF format, chain RA [auth F] SDF format, chain U [auth B] SDF format, chain XA [auth G] MOL2 format, chain CC [auth L] MOL2 format, chain DB [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain WB [auth K] MOL2 format, chain JB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PB [auth J] MOL2 format, chain RA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain XA [auth G]	CC [auth L] DB [auth H] FA [auth D] JB [auth I] LA [auth E] CC [auth L], DB [auth H], FA [auth D], JB [auth I], LA [auth E], N [auth A], O [auth A], PB [auth J], RA [auth F], U [auth B], WB [auth K], XA [auth G]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain CC [auth L] Focus chain DB [auth H] Focus chain FA [auth D] Focus chain JB [auth I] Focus chain LA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain PB [auth J] Focus chain RA [auth F] Focus chain U [auth B] Focus chain WB [auth K] Focus chain XA [auth G] Interactions & Density Focus chain CC [auth L] Focus chain DB [auth H] Focus chain FA [auth D] Focus chain JB [auth I] Focus chain LA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain PB [auth J] Focus chain RA [auth F] Focus chain U [auth B] Focus chain WB [auth K] Focus chain XA [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BC [auth L] SDF format, chain CB [auth H] SDF format, chain EA [auth D] SDF format, chain IB [auth I] SDF format, chain M [auth A] SDF format, chain OB [auth J] SDF format, chain QA [auth F] SDF format, chain T [auth B] SDF format, chain Z [auth C] SDF format, chain KA [auth E] SDF format, chain VB [auth K] SDF format, chain WA [auth G] MOL2 format, chain BC [auth L] MOL2 format, chain CB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain IB [auth I] MOL2 format, chain M [auth A] MOL2 format, chain OB [auth J] MOL2 format, chain QA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain VB [auth K] MOL2 format, chain WA [auth G]	BC [auth L] CB [auth H] EA [auth D] IB [auth I] KA [auth E] BC [auth L], CB [auth H], EA [auth D], IB [auth I], KA [auth E], M [auth A], OB [auth J], QA [auth F], T [auth B], VB [auth K], WA [auth G], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BC [auth L] Focus chain CB [auth H] Focus chain EA [auth D] Focus chain IB [auth I] Focus chain KA [auth E] Focus chain M [auth A] Focus chain OB [auth J] Focus chain QA [auth F] Focus chain T [auth B] Focus chain VB [auth K] Focus chain WA [auth G] Focus chain Z [auth C] Interactions & Density Focus chain BC [auth L] Focus chain CB [auth H] Focus chain EA [auth D] Focus chain IB [auth I] Focus chain KA [auth E] Focus chain M [auth A] Focus chain OB [auth J] Focus chain QA [auth F] Focus chain T [auth B] Focus chain VB [auth K] Focus chain WA [auth G] Focus chain Z [auth C]
BEZ Query on BEZ Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain CA [auth C] SDF format, chain FC [auth L] SDF format, chain JA [auth D] SDF format, chain NB [auth I] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain TB [auth J] SDF format, chain UA [auth F] SDF format, chain X [auth B] SDF format, chain ZB [auth K] SDF format, chain AC [auth K] SDF format, chain BB [auth G] SDF format, chain DA [auth C] SDF format, chain EC [auth L] SDF format, chain GB [auth H] SDF format, chain HB [auth H] SDF format, chain IA [auth D] SDF format, chain MB [auth I] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain UB [auth J] SDF format, chain VA [auth F] SDF format, chain Y [auth B] MOL2 format, chain AB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain FC [auth L] MOL2 format, chain JA [auth D] MOL2 format, chain NB [auth I] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain TB [auth J] MOL2 format, chain UA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain ZB [auth K] MOL2 format, chain AC [auth K] MOL2 format, chain BB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain EC [auth L] MOL2 format, chain GB [auth H] MOL2 format, chain HB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain MB [auth I] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain UB [auth J] MOL2 format, chain VA [auth F] MOL2 format, chain Y [auth B]	AB [auth G] AC [auth K] BB [auth G] CA [auth C] DA [auth C] AB [auth G], AC [auth K], BB [auth G], CA [auth C], DA [auth C], EC [auth L], FC [auth L], GB [auth H], HB [auth H], IA [auth D], JA [auth D], MB [auth I], NB [auth I], OA [auth E], PA [auth E], R [auth A], S [auth A], TB [auth J], UA [auth F], UB [auth J], VA [auth F], X [auth B], Y [auth B], ZB [auth K]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain AC [auth K] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EC [auth L] Focus chain FC [auth L] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain MB [auth I] Focus chain NB [auth I] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain R [auth A] Focus chain S [auth A] Focus chain TB [auth J] Focus chain UA [auth F] Focus chain UB [auth J] Focus chain VA [auth F] Focus chain X [auth B] Focus chain Y [auth B] Focus chain ZB [auth K] Interactions & Density Focus chain AB [auth G] Focus chain AC [auth K] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EC [auth L] Focus chain FC [auth L] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain MB [auth I] Focus chain NB [auth I] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain R [auth A] Focus chain S [auth A] Focus chain TB [auth J] Focus chain UA [auth F] Focus chain UB [auth J] Focus chain VA [auth F] Focus chain X [auth B] Focus chain Y [auth B] Focus chain ZB [auth K]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain FB [auth H] SDF format, chain HA [auth D] SDF format, chain LB [auth I] SDF format, chain P [auth A] SDF format, chain RB [auth J] SDF format, chain TA [auth F] SDF format, chain XB [auth K] SDF format, chain YB [auth K] SDF format, chain ZA [auth G] SDF format, chain AA [auth C] SDF format, chain DC [auth L] SDF format, chain EB [auth H] SDF format, chain GA [auth D] SDF format, chain KB [auth I] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain Q [auth A] SDF format, chain QB [auth J] SDF format, chain SA [auth F] SDF format, chain SB [auth J] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain YA [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain FB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain LB [auth I] MOL2 format, chain P [auth A] MOL2 format, chain RB [auth J] MOL2 format, chain TA [auth F] MOL2 format, chain XB [auth K] MOL2 format, chain YB [auth K] MOL2 format, chain ZA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain DC [auth L] MOL2 format, chain EB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain KB [auth I] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth J] MOL2 format, chain SA [auth F] MOL2 format, chain SB [auth J] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain YA [auth G]	AA [auth C] BA [auth C] DC [auth L] EB [auth H] FB [auth H] AA [auth C], BA [auth C], DC [auth L], EB [auth H], FB [auth H], GA [auth D], HA [auth D], KB [auth I], LB [auth I], MA [auth E], NA [auth E], P [auth A], Q [auth A], QB [auth J], RB [auth J], SA [auth F], SB [auth J], TA [auth F], V [auth B], W [auth B], XB [auth K], YA [auth G], YB [auth K], ZA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DC [auth L] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QB [auth J] Focus chain RB [auth J] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain TA [auth F] Focus chain V [auth B] Focus chain W [auth B] Focus chain XB [auth K] Focus chain YA [auth G] Focus chain YB [auth K] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DC [auth L] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain KB [auth I] Focus chain LB [auth I] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QB [auth J] Focus chain RB [auth J] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain TA [auth F] Focus chain V [auth B] Focus chain W [auth B] Focus chain XB [auth K] Focus chain YA [auth G] Focus chain YB [auth K] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.287
R-Value Work: 0.207
R-Value Observed: 0.207
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.56	α = 90.1195
b = 181.493	β = 89.9291
c = 202.712	γ = 89.7185

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-08-02

Deposition Author(s):

Howard-Williams, E.L.

Potter, P.M.

Redinbo, M.R.

Revision History (Full details and data files)

Version 1.0: 2005-08-02
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary