9WF6 | pdb_00009wf6

Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue-3.0 A

PDB DOI: https://doi.org/10.2210/pdb9WF6/pdb

Classification: CHAPERONE
Organism(s): Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-21 Released: 2025-09-03
Deposition Author(s): Guo, Y., Zhang, L., Zheng, H., Li, J., Han, Q.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free:
0.236 (Depositor), 0.233 (DCC)
R-Value Work:
0.205 (Depositor), 0.203 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue

Guo, Y., Zhang, L., Zheng, H., Li, J., Han, Q.

To be published.

Macromolecule Content

Total Structure Weight: 1,617.07 kDa
Atom Count: 108,950
Modeled Residue Count: 14,698
Deposited Residue Count: 15,344
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin GroEL	A AA [auth b] B C F A, AA [auth b], B, C, F, G, H, I, J, M, N, P, Q, S [auth T], T [auth U], X [auth Y], Z [auth a]	548	Escherichia coli BL21(DE3)	Mutation(s): 0 EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12)) Explore P0A6F5 Go to UniProtKB: P0A6F5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6F5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin GroEL	BA [auth c] D E K L BA [auth c], D, E, K, L, O, R, U [auth V], V [auth W], W [auth X], Y [auth Z]	548	Escherichia coli BL21(DE3)	Mutation(s): 0 EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12)) Explore P0A6F5 Go to UniProtKB: P0A6F5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6F5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain YB [auth N] SDF format, chain XC [auth U] SDF format, chain XA [auth E] SDF format, chain WD [auth c] SDF format, chain WA [auth E] SDF format, chain VD [auth c] SDF format, chain VB [auth M] SDF format, chain VA [auth E] SDF format, chain UD [auth c] SDF format, chain TB [auth L] SDF format, chain SC [auth T] SDF format, chain SB [auth K] SDF format, chain RC [auth T] SDF format, chain QB [auth J] SDF format, chain QA [auth D] SDF format, chain PD [auth b] SDF format, chain PC [auth R] SDF format, chain PA [auth D] SDF format, chain OC [auth R] SDF format, chain OB [auth I] SDF format, chain ND [auth a] SDF format, chain NB [auth I] SDF format, chain LD [auth Z] SDF format, chain LC [auth Q] SDF format, chain LA [auth C] SDF format, chain KB [auth H] SDF format, chain JD [auth Y] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HD [auth X] SDF format, chain HC [auth P] SDF format, chain HB [auth G] SDF format, chain ED [auth W] SDF format, chain EC [auth O] SDF format, chain EA [auth A] SDF format, chain DD [auth W] SDF format, chain DC [auth O] SDF format, chain DA [auth A] SDF format, chain BD [auth V] SDF format, chain BB [auth F] SDF format, chain AD [auth V] SDF format, chain AB [auth F] MOL2 format, chain YB [auth N] MOL2 format, chain XC [auth U] MOL2 format, chain XA [auth E] MOL2 format, chain WD [auth c] MOL2 format, chain WA [auth E] MOL2 format, chain VD [auth c] MOL2 format, chain VB [auth M] MOL2 format, chain VA [auth E] MOL2 format, chain UD [auth c] MOL2 format, chain TB [auth L] MOL2 format, chain SC [auth T] MOL2 format, chain SB [auth K] MOL2 format, chain RC [auth T] MOL2 format, chain QB [auth J] MOL2 format, chain QA [auth D] MOL2 format, chain PD [auth b] MOL2 format, chain PC [auth R] MOL2 format, chain PA [auth D] MOL2 format, chain OC [auth R] MOL2 format, chain OB [auth I] MOL2 format, chain ND [auth a] MOL2 format, chain NB [auth I] MOL2 format, chain LD [auth Z] MOL2 format, chain LC [auth Q] MOL2 format, chain LA [auth C] MOL2 format, chain KB [auth H] MOL2 format, chain JD [auth Y] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HD [auth X] MOL2 format, chain HC [auth P] MOL2 format, chain HB [auth G] MOL2 format, chain ED [auth W] MOL2 format, chain EC [auth O] MOL2 format, chain EA [auth A] MOL2 format, chain DD [auth W] MOL2 format, chain DC [auth O] MOL2 format, chain DA [auth A] MOL2 format, chain BD [auth V] MOL2 format, chain BB [auth F] MOL2 format, chain AD [auth V] MOL2 format, chain AB [auth F] mmCIF format, chain YB [auth N] mmCIF format, chain XC [auth U] mmCIF format, chain XA [auth E] mmCIF format, chain WD [auth c] mmCIF format, chain WA [auth E] mmCIF format, chain VD [auth c] mmCIF format, chain VB [auth M] mmCIF format, chain VA [auth E] mmCIF format, chain UD [auth c] mmCIF format, chain TB [auth L] mmCIF format, chain SC [auth T] mmCIF format, chain SB [auth K] mmCIF format, chain RC [auth T] mmCIF format, chain QB [auth J] mmCIF format, chain QA [auth D] mmCIF format, chain PD [auth b] mmCIF format, chain PC [auth R] mmCIF format, chain PA [auth D] mmCIF format, chain OC [auth R] mmCIF format, chain OB [auth I] mmCIF format, chain ND [auth a] mmCIF format, chain NB [auth I] mmCIF format, chain LD [auth Z] mmCIF format, chain LC [auth Q] mmCIF format, chain LA [auth C] mmCIF format, chain KB [auth H] mmCIF format, chain JD [auth Y] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HD [auth X] mmCIF format, chain HC [auth P] mmCIF format, chain HB [auth G] mmCIF format, chain ED [auth W] mmCIF format, chain EC [auth O] mmCIF format, chain EA [auth A] mmCIF format, chain DD [auth W] mmCIF format, chain DC [auth O] mmCIF format, chain DA [auth A] mmCIF format, chain BD [auth V] mmCIF format, chain BB [auth F] mmCIF format, chain AD [auth V] mmCIF format, chain AB [auth F]	AB [auth F] AD [auth V] BB [auth F] BD [auth V] DA [auth A] AB [auth F], AD [auth V], BB [auth F], BD [auth V], DA [auth A], DC [auth O], DD [auth W], EA [auth A], EC [auth O], ED [auth W], HB [auth G], HC [auth P], HD [auth X], IA [auth B], JA [auth B], JD [auth Y], KB [auth H], LA [auth C], LC [auth Q], LD [auth Z], NB [auth I], ND [auth a], OB [auth I], OC [auth R], PA [auth D], PC [auth R], PD [auth b], QA [auth D], QB [auth J], RC [auth T], SB [auth K], SC [auth T], TB [auth L], UD [auth c], VA [auth E], VB [auth M], VD [auth c], WA [auth E], WD [auth c], XA [auth E], XC [auth U], YB [auth N]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain AD [auth V] Focus chain BB [auth F] Focus chain BD [auth V] Focus chain DA [auth A] Focus chain DC [auth O] Focus chain DD [auth W] Focus chain EA [auth A] Focus chain EC [auth O] Focus chain ED [auth W] Focus chain HB [auth G] Focus chain HC [auth P] Focus chain HD [auth X] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JD [auth Y] Focus chain KB [auth H] Focus chain LA [auth C] Focus chain LC [auth Q] Focus chain LD [auth Z] Focus chain NB [auth I] Focus chain ND [auth a] Focus chain OB [auth I] Focus chain OC [auth R] Focus chain PA [auth D] Focus chain PC [auth R] Focus chain PD [auth b] Focus chain QA [auth D] Focus chain QB [auth J] Focus chain RC [auth T] Focus chain SB [auth K] Focus chain SC [auth T] Focus chain TB [auth L] Focus chain UD [auth c] Focus chain VA [auth E] Focus chain VB [auth M] Focus chain VD [auth c] Focus chain WA [auth E] Focus chain WD [auth c] Focus chain XA [auth E] Focus chain XC [auth U] Focus chain YB [auth N] Interactions & Density Focus chain AB [auth F] Focus chain AD [auth V] Focus chain BB [auth F] Focus chain BD [auth V] Focus chain DA [auth A] Focus chain DC [auth O] Focus chain DD [auth W] Focus chain EA [auth A] Focus chain EC [auth O] Focus chain ED [auth W] Focus chain HB [auth G] Focus chain HC [auth P] Focus chain HD [auth X] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain JD [auth Y] Focus chain KB [auth H] Focus chain LA [auth C] Focus chain LC [auth Q] Focus chain LD [auth Z] Focus chain NB [auth I] Focus chain ND [auth a] Focus chain OB [auth I] Focus chain OC [auth R] Focus chain PA [auth D] Focus chain PC [auth R] Focus chain PD [auth b] Focus chain QA [auth D] Focus chain QB [auth J] Focus chain RC [auth T] Focus chain SB [auth K] Focus chain SC [auth T] Focus chain TB [auth L] Focus chain UD [auth c] Focus chain VA [auth E] Focus chain VB [auth M] Focus chain VD [auth c] Focus chain WA [auth E] Focus chain WD [auth c] Focus chain XA [auth E] Focus chain XC [auth U] Focus chain YB [auth N]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain ZC [auth V] SDF format, chain ZA [auth F] SDF format, chain XB [auth N] SDF format, chain WC [auth U] SDF format, chain VC [auth U] SDF format, chain UC [auth U] SDF format, chain UB [auth M] SDF format, chain UA [auth E] SDF format, chain TD [auth c] SDF format, chain TA [auth E] SDF format, chain SD [auth c] SDF format, chain SA [auth E] SDF format, chain RD [auth c] SDF format, chain RB [auth K] SDF format, chain QC [auth T] SDF format, chain PB [auth J] SDF format, chain OD [auth b] SDF format, chain OA [auth D] SDF format, chain NC [auth R] SDF format, chain NA [auth D] SDF format, chain MD [auth a] SDF format, chain MC [auth R] SDF format, chain MA [auth D] SDF format, chain KD [auth Z] SDF format, chain KC [auth Q] SDF format, chain KA [auth C] SDF format, chain JC [auth Q] SDF format, chain JB [auth H] SDF format, chain ID [auth Y] SDF format, chain IC [auth Q] SDF format, chain HA [auth B] SDF format, chain GD [auth X] SDF format, chain GC [auth P] SDF format, chain GB [auth G] SDF format, chain GA [auth B] SDF format, chain FD [auth X] SDF format, chain FC [auth P] SDF format, chain FB [auth G] SDF format, chain EB [auth G] SDF format, chain DB [auth G] SDF format, chain CC [auth O] SDF format, chain CA [auth A] SDF format, chain BC [auth O] SDF format, chain AC [auth O] MOL2 format, chain ZC [auth V] MOL2 format, chain ZA [auth F] MOL2 format, chain XB [auth N] MOL2 format, chain WC [auth U] MOL2 format, chain VC [auth U] MOL2 format, chain UC [auth U] MOL2 format, chain UB [auth M] MOL2 format, chain UA [auth E] MOL2 format, chain TD [auth c] MOL2 format, chain TA [auth E] MOL2 format, chain SD [auth c] MOL2 format, chain SA [auth E] MOL2 format, chain RD [auth c] MOL2 format, chain RB [auth K] MOL2 format, chain QC [auth T] MOL2 format, chain PB [auth J] MOL2 format, chain OD [auth b] MOL2 format, chain OA [auth D] MOL2 format, chain NC [auth R] MOL2 format, chain NA [auth D] MOL2 format, chain MD [auth a] MOL2 format, chain MC [auth R] MOL2 format, chain MA [auth D] MOL2 format, chain KD [auth Z] MOL2 format, chain KC [auth Q] MOL2 format, chain KA [auth C] MOL2 format, chain JC [auth Q] MOL2 format, chain JB [auth H] MOL2 format, chain ID [auth Y] MOL2 format, chain IC [auth Q] MOL2 format, chain HA [auth B] MOL2 format, chain GD [auth X] MOL2 format, chain GC [auth P] MOL2 format, chain GB [auth G] MOL2 format, chain GA [auth B] MOL2 format, chain FD [auth X] MOL2 format, chain FC [auth P] MOL2 format, chain FB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain CC [auth O] MOL2 format, chain CA [auth A] MOL2 format, chain BC [auth O] MOL2 format, chain AC [auth O] mmCIF format, chain ZC [auth V] mmCIF format, chain ZA [auth F] mmCIF format, chain XB [auth N] mmCIF format, chain WC [auth U] mmCIF format, chain VC [auth U] mmCIF format, chain UC [auth U] mmCIF format, chain UB [auth M] mmCIF format, chain UA [auth E] mmCIF format, chain TD [auth c] mmCIF format, chain TA [auth E] mmCIF format, chain SD [auth c] mmCIF format, chain SA [auth E] mmCIF format, chain RD [auth c] mmCIF format, chain RB [auth K] mmCIF format, chain QC [auth T] mmCIF format, chain PB [auth J] mmCIF format, chain OD [auth b] mmCIF format, chain OA [auth D] mmCIF format, chain NC [auth R] mmCIF format, chain NA [auth D] mmCIF format, chain MD [auth a] mmCIF format, chain MC [auth R] mmCIF format, chain MA [auth D] mmCIF format, chain KD [auth Z] mmCIF format, chain KC [auth Q] mmCIF format, chain KA [auth C] mmCIF format, chain JC [auth Q] mmCIF format, chain JB [auth H] mmCIF format, chain ID [auth Y] mmCIF format, chain IC [auth Q] mmCIF format, chain HA [auth B] mmCIF format, chain GD [auth X] mmCIF format, chain GC [auth P] mmCIF format, chain GB [auth G] mmCIF format, chain GA [auth B] mmCIF format, chain FD [auth X] mmCIF format, chain FC [auth P] mmCIF format, chain FB [auth G] mmCIF format, chain EB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain CC [auth O] mmCIF format, chain CA [auth A] mmCIF format, chain BC [auth O] mmCIF format, chain AC [auth O]	AC [auth O] BC [auth O] CA [auth A] CC [auth O] DB [auth G] AC [auth O], BC [auth O], CA [auth A], CC [auth O], DB [auth G], EB [auth G], FB [auth G], FC [auth P], FD [auth X], GA [auth B], GB [auth G], GC [auth P], GD [auth X], HA [auth B], IC [auth Q], ID [auth Y], JB [auth H], JC [auth Q], KA [auth C], KC [auth Q], KD [auth Z], MA [auth D], MC [auth R], MD [auth a], NA [auth D], NC [auth R], OA [auth D], OD [auth b], PB [auth J], QC [auth T], RB [auth K], RD [auth c], SA [auth E], SD [auth c], TA [auth E], TD [auth c], UA [auth E], UB [auth M], UC [auth U], VC [auth U], WC [auth U], XB [auth N], ZA [auth F], ZC [auth V]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain AC [auth O] Focus chain BC [auth O] Focus chain CA [auth A] Focus chain CC [auth O] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain FC [auth P] Focus chain FD [auth X] Focus chain GA [auth B] Focus chain GB [auth G] Focus chain GC [auth P] Focus chain GD [auth X] Focus chain HA [auth B] Focus chain IC [auth Q] Focus chain ID [auth Y] Focus chain JB [auth H] Focus chain JC [auth Q] Focus chain KA [auth C] Focus chain KC [auth Q] Focus chain KD [auth Z] Focus chain MA [auth D] Focus chain MC [auth R] Focus chain MD [auth a] Focus chain NA [auth D] Focus chain NC [auth R] Focus chain OA [auth D] Focus chain OD [auth b] Focus chain PB [auth J] Focus chain QC [auth T] Focus chain RB [auth K] Focus chain RD [auth c] Focus chain SA [auth E] Focus chain SD [auth c] Focus chain TA [auth E] Focus chain TD [auth c] Focus chain UA [auth E] Focus chain UB [auth M] Focus chain UC [auth U] Focus chain VC [auth U] Focus chain WC [auth U] Focus chain XB [auth N] Focus chain ZA [auth F] Focus chain ZC [auth V] Interactions & Density Focus chain AC [auth O] Focus chain BC [auth O] Focus chain CA [auth A] Focus chain CC [auth O] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FB [auth G] Focus chain FC [auth P] Focus chain FD [auth X] Focus chain GA [auth B] Focus chain GB [auth G] Focus chain GC [auth P] Focus chain GD [auth X] Focus chain HA [auth B] Focus chain IC [auth Q] Focus chain ID [auth Y] Focus chain JB [auth H] Focus chain JC [auth Q] Focus chain KA [auth C] Focus chain KC [auth Q] Focus chain KD [auth Z] Focus chain MA [auth D] Focus chain MC [auth R] Focus chain MD [auth a] Focus chain NA [auth D] Focus chain NC [auth R] Focus chain OA [auth D] Focus chain OD [auth b] Focus chain PB [auth J] Focus chain QC [auth T] Focus chain RB [auth K] Focus chain RD [auth c] Focus chain SA [auth E] Focus chain SD [auth c] Focus chain TA [auth E] Focus chain TD [auth c] Focus chain UA [auth E] Focus chain UB [auth M] Focus chain UC [auth U] Focus chain VC [auth U] Focus chain WC [auth U] Focus chain XB [auth N] Focus chain ZA [auth F] Focus chain ZC [auth V]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain ZB [auth N] SDF format, chain YC [auth U] SDF format, chain YA [auth E] SDF format, chain XD [auth c] SDF format, chain WB [auth M] SDF format, chain TC [auth T] SDF format, chain RA [auth D] SDF format, chain QD [auth b] SDF format, chain MB [auth H] SDF format, chain LB [auth H] SDF format, chain IB [auth G] SDF format, chain FA [auth A] SDF format, chain CD [auth V] SDF format, chain CB [auth F] MOL2 format, chain ZB [auth N] MOL2 format, chain YC [auth U] MOL2 format, chain YA [auth E] MOL2 format, chain XD [auth c] MOL2 format, chain WB [auth M] MOL2 format, chain TC [auth T] MOL2 format, chain RA [auth D] MOL2 format, chain QD [auth b] MOL2 format, chain MB [auth H] MOL2 format, chain LB [auth H] MOL2 format, chain IB [auth G] MOL2 format, chain FA [auth A] MOL2 format, chain CD [auth V] MOL2 format, chain CB [auth F] mmCIF format, chain ZB [auth N] mmCIF format, chain YC [auth U] mmCIF format, chain YA [auth E] mmCIF format, chain XD [auth c] mmCIF format, chain WB [auth M] mmCIF format, chain TC [auth T] mmCIF format, chain RA [auth D] mmCIF format, chain QD [auth b] mmCIF format, chain MB [auth H] mmCIF format, chain LB [auth H] mmCIF format, chain IB [auth G] mmCIF format, chain FA [auth A] mmCIF format, chain CD [auth V] mmCIF format, chain CB [auth F]	CB [auth F] CD [auth V] FA [auth A] IB [auth G] LB [auth H] CB [auth F], CD [auth V], FA [auth A], IB [auth G], LB [auth H], MB [auth H], QD [auth b], RA [auth D], TC [auth T], WB [auth M], XD [auth c], YA [auth E], YC [auth U], ZB [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Focus chain CD [auth V] Focus chain FA [auth A] Focus chain IB [auth G] Focus chain LB [auth H] Focus chain MB [auth H] Focus chain QD [auth b] Focus chain RA [auth D] Focus chain TC [auth T] Focus chain WB [auth M] Focus chain XD [auth c] Focus chain YA [auth E] Focus chain YC [auth U] Focus chain ZB [auth N] Interactions & Density Focus chain CB [auth F] Focus chain CD [auth V] Focus chain FA [auth A] Focus chain IB [auth G] Focus chain LB [auth H] Focus chain MB [auth H] Focus chain QD [auth b] Focus chain RA [auth D] Focus chain TC [auth T] Focus chain WB [auth M] Focus chain XD [auth c] Focus chain YA [auth E] Focus chain YC [auth U] Focus chain ZB [auth N]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A AA [auth b] B C F A, AA [auth b], B, C, F, G, H, I, J, M, N, P, Q, S [auth T], T [auth U], X [auth Y], Z [auth a]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.236 (Depositor), 0.233 (DCC)
R-Value Work: 0.205 (Depositor), 0.203 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 285.871	α = 90
b = 136.256	β = 117.11
c = 287.795	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS062836
National Natural Science Foundation of China (NSFC)	China	31860702