1DKD: Groel

Crystal structure of a groel (apical domain) and a dodecameric peptide complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 12 Jan 2000.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Escherichia coli
Chains: 8
Atoms: 4,818
Mol. weight: 68.76 kDa
Released: 12 Jan 2000

Explore 1DKD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DKD contains 34 α-helices and 60 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	193-195	3	1
α-helix	202-204	3
β-strand	207	1	2
β-strand	212	1	2
β-strand	213-216	4	1
β-strand	219-222	4	3
β-strand	223	1	4
β-strand	226-227	2	5
α-helix	230-233	4
α-helix	234-243	10
β-strand	247-251	5	3
β-strand	253-254	2	5
α-helix	256-267	12
β-strand	273-277	5	3
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	4
α-helix	309-311	3
α-helix	314-316	3
β-strand	318-319	2	3
β-strand	320-325	6	1
β-strand	330-335	6	1

Chain B: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	192-195	4	7
β-strand	199	1	8
α-helix	202-204	3
β-strand	207	1	9
β-strand	212	1	9
β-strand	213-216	4	7
β-strand	219-227	9	8
α-helix	230-232	3
α-helix	234-243	10
β-strand	247-254	8	8
α-helix	256-267	12
β-strand	273-277	5	8
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	8
α-helix	303-305	3
α-helix	309-311	3
α-helix	314-316	3
β-strand	318-319	2	8
β-strand	320-325	6	7
β-strand	330-335	6	7

Chain C: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	193-195	3	11
β-strand	199	1	12
α-helix	202-204	3
β-strand	207	1	13
β-strand	212	1	13
β-strand	213-216	4	11
β-strand	219-227	9	12
α-helix	230-232	3
α-helix	234-243	10
β-strand	247-254	8	12
α-helix	256-267	12
β-strand	273-277	5	12
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	12
α-helix	309-311	3
α-helix	314-316	3
β-strand	318-319	2	12
β-strand	320-325	6	11
β-strand	330-335	6	11

Chain D: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	193-195	3	15
α-helix	202-204	3
β-strand	207	1	16
β-strand	212	1	16
β-strand	213-216	4	15
β-strand	219-222	4	17
β-strand	223	1	18
β-strand	226-227	2	19
α-helix	230-233	4
α-helix	234-242	9
β-strand	247-251	5	17
β-strand	253-254	2	19
α-helix	256-267	12
β-strand	273-277	5	17
α-helix	278	1
α-helix	282-296	15
β-strand	301	1	18
α-helix	303-305	3
α-helix	309-311	3
α-helix	314-316	3
β-strand	318-319	2	17
β-strand	320-325	6	15
β-strand	330-335	6	15

Chains E, F, G and H: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	603-604	2	6
β-strand	610-611	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Groel	A, B, C, D	protein	146	Escherichia coli	P0A6F5 (AlphaFold model)
12-mer peptide	E, F, G, H	protein	12

Sequence of entity 1 (A, B, C, D), FASTA

>1DKD_1 GROEL (chains A, B, C, D)
EGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLII
AEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELE
KATLEDLGQAKRVVINKDTTTIIDGV

Sequence of entity 2 (E, F, G, H), FASTA

>1DKD_2 12-MER PEPTIDE (chains E, F, G, H)
SWMTTPWGFLHP

Primary citation

The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity. Chen, L., Sigler, P.B. Cell (1999) 99:757-768. DOI 10.1016/S0092-8674(00)81673-6 · PubMed

Other PDB entries of the same protein (UniProt P0A6F5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VZ6 1.5 Å, Crystal Structure Analysis of the Mini-chaperonines, variant with Gly 184 replaced with…
1KID 1.7 Å, Groel (HSP60 class) fragment (apical domain) comprising residues 191-376, mutant with…
3VZ7 1.8 Å, Crystal Structure Analysis of the mini-chaperonin variant with Pro 187 Gly
3VZ8 1.9 Å, Crystal Structure Analysis of the Mini-chaperonin variant with Leu 185, Val 186, Pro…
1KP8 2.0 Å, Structural Basis for GroEL-assisted Protein Folding from the Crystal Structure of…
1SX3 2.0 Å, GroEL14-(ATPgammaS)14
1DK7 2.02 Å, Crystal structure of an isolated apical domain of groel
1LA1 2.06 Å, Gro-EL Fragment (Apical Domain) Comprising Residues 188-379
1FY9 2.2 Å, Crystal structure of the hexa-substituted mutant of the molecular chaperonin groel…
1FYA 2.2 Å, Crystal structure of the hexa-substituted mutant of the molecular chaperonin groel…
8BKZ 2.3 Å, GroEL:GroES-ATP complex under continuous turnover conditions
8BL2 2.3 Å, Structure of GroEL-ATP complex plunge frozen 200 ms after reaction initiation

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