1WA3: Mechanism of the Class I KDPG aldolase

Mechanism of the Class I KDPG aldolase. Determined by X-ray diffraction at 1.9 Å resolution. Released 26 Jan 2005.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: THERMOTOGA MARITIMA
Chains: 6
Atoms: 9,569
Mol. weight: 134.71 kDa
Ligands: PYR
Released: 26 Jan 2005

Explore 1WA3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1WA3 contains 68 α-helices and 60 β-strands across 6 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: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	12-16	5	1
α-helix	21-33	13
β-strand	38-42	5	1
α-helix	48-54	7
α-helix	56-60	5
β-strand	64-68	5	1
α-helix	73-82	10
β-strand	86-88	3	1
α-helix	94-103	10
β-strand	106-108	3	1
β-strand	110-111	2	2
α-helix	114-122	9
β-strand	127-130	4	2
α-helix	133-145	13
β-strand	152-155	4	2
β-strand	156	1	1
α-helix	164-170	7
β-strand	175-177	3	1
α-helix	179-182	4
α-helix	186-202	17

Chain B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	12-16	5	3
α-helix	21-33	13
β-strand	38-42	5	3
α-helix	48-54	7
α-helix	56-61	6
β-strand	64-68	5	3
α-helix	73-81	9
β-strand	86-88	3	3
α-helix	94-103	10
β-strand	106-108	3	3
β-strand	110-111	2	4
α-helix	114-122	9
β-strand	127-130	4	4
α-helix	133-145	13
β-strand	152-155	4	4
β-strand	156	1	3
α-helix	164-170	7
β-strand	175-177	3	3
α-helix	179-182	4
α-helix	186-202	17

Chain C: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
β-strand	12-16	5	5
α-helix	21-33	13
β-strand	38-42	5	5
α-helix	48-55	8
α-helix	56-61	6
β-strand	64-68	5	5
α-helix	73-81	9
β-strand	86-88	3	5
α-helix	94-103	10
β-strand	106-108	3	5
β-strand	110-111	2	6
α-helix	114-122	9
β-strand	127-130	4	6
α-helix	133-145	13
β-strand	152-155	4	6
β-strand	156	1	5
α-helix	164-170	7
β-strand	175-177	3	5
α-helix	179-182	4
α-helix	186-201	16

Chain D: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	12-16	5	7
α-helix	21-33	13
β-strand	38-42	5	7
α-helix	48-54	7
α-helix	56-60	5
β-strand	64-68	5	7
α-helix	73-81	9
β-strand	86-88	3	7
α-helix	94-103	10
β-strand	106-108	3	7
β-strand	110-111	2	8
α-helix	114-122	9
β-strand	127-130	4	8
α-helix	133-136	4
α-helix	138-145	8
β-strand	152-155	4	8
β-strand	156	1	7
α-helix	164-169	6
β-strand	175-177	3	7
α-helix	179-182	4
α-helix	186-203	18

Chain E: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	12-16	5	9
α-helix	21-33	13
β-strand	38-42	5	9
α-helix	48-54	7
α-helix	56-59	4
β-strand	64-68	5	9
α-helix	73-81	9
β-strand	86-88	3	9
α-helix	94-103	10
β-strand	106-108	3	9
β-strand	110-111	2	10
α-helix	114-122	9
β-strand	127-130	4	10
α-helix	133-136	4
α-helix	138-144	7
β-strand	152-155	4	10
β-strand	156	1	9
α-helix	164-169	6
β-strand	175-177	3	9
α-helix	179-182	4
α-helix	186-202	17

Chain F: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
β-strand	12-16	5	11
α-helix	21-34	14
β-strand	38-42	5	11
α-helix	48-54	7
α-helix	57-60	4
β-strand	64-68	5	11
α-helix	73-81	9
β-strand	86-88	3	11
α-helix	94-103	10
β-strand	106-108	3	11
β-strand	110-111	2	12
α-helix	114-122	9
β-strand	127-130	4	12
α-helix	133-145	13
β-strand	152-155	4	12
β-strand	156	1	11
α-helix	164-170	7
β-strand	175-177	3	11
α-helix	179-182	4
α-helix	186-201	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2-keto-3-deoxy-6-phosphogluconate aldolase	A, B, C, D, E, F	protein	205	THERMOTOGA MARITIMA	Q9WXS1 (AlphaFold model)

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

>1WA3_1 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE (chains A, B, C, D, E, F)
MKMEELFKKHKIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLKE
KGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKA
MKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSA
LVKGTPDEVREKAKAFVEKIRGCTE

Ligands and cofactors

ID	Name	Formula	Copies
PYR	Pyruvic acid	C3 H4 O3	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

Mechanism of the Class I Kdpg Aldolase. Fullerton, S.W.B., Griffiths, J.S., Merkel, A.B. et al. Bioorg Med Chem (2006) 14:3002. DOI 10.1016/J.BMC.2005.12.022 · PubMed

Other PDB entries of the same protein (UniProt Q9WXS1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9UAQ 2.29 Å, CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
1VLW 2.3 Å, Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate…
9UCL 2.43 Å, CryoEM structure of IgV domain of human Nectin-4 with Trimbody
9XOU 2.5 Å, CryoEM structure of LacY with Trimbody
9UBR 2.62 Å, CryoEM structure of human Galectin-10 with iTrimbody
8SZZ 2.9 Å, CryoEM Structure of Computationally Designed Nanocage O32-ZL4
8TVB 2.9 Å, Ghanaian virus fusion glycoprotein (GhV F)
8TYC 3.3 Å, Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1
8E01 3.4 Å, Structure of engineered nano-cage fusion protein
8JGC 3.44 Å, Cryo-EM structure of Mi3 fused with LOV2
8JGA 3.68 Å, Cryo-EM structure of Mi3 fused with FKBP
7B3Y 3.7 Å, Structure of a nanoparticle for a COVID-19 vaccine candidate

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