6Y4Z: Human MACROD2 in space group P43212

The crystal structure of human MACROD2 in space group P43212. Determined by X-ray diffraction at 1.9 Å resolution. Released 30 Sept 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Escherichia coli (strain K12), Homo sapiens
Chains: 4
Atoms: 7,372
Mol. weight: 163.78 kDa
Ligands: TLA
Released: 30 Sept 2020

Explore 6Y4Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y4Z contains 54 α-helices and 36 β-strands across 4 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: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	12
α-helix	23-28	6
β-strand	35-36	2	1
α-helix	37-39	3
α-helix	41-42	2
α-helix	43-48	6
α-helix	68-70	3
β-strand	72-75	4	2
α-helix	79-81	3
β-strand	82-83	2	1
β-strand	86-91	6	2
α-helix	100-109	10
α-helix	111-119	9
β-strand	125	1	2
β-strand	128-132	5	2
β-strand	140-145	6	2
α-helix	155-174	20
β-strand	179-182	4	2
α-helix	188-190	3
α-helix	194-212	19
α-helix	213-215	3
β-strand	218-222	5	2
α-helix	226-240	15

Chain B: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
α-helix	23-29	7
β-strand	35-36	2	3
α-helix	37-39	3
α-helix	41-42	2
α-helix	43-46	4
α-helix	68-70	3
β-strand	72-76	5	4
α-helix	79-81	3
β-strand	82-83	2	3
β-strand	86-91	6	4
α-helix	100-109	10
α-helix	111-118	8
β-strand	125	1	4
β-strand	128-132	5	4
β-strand	140-145	6	4
α-helix	155-174	20
β-strand	179-182	4	4
α-helix	188-190	3
α-helix	194-212	19
α-helix	213-215	3
β-strand	218-223	6	4
α-helix	226-240	15

Chain C: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
α-helix	23-27	5
β-strand	35-36	2	5
α-helix	37-39	3
α-helix	43-47	5
α-helix	68-70	3
β-strand	72-76	5	6
α-helix	79-81	3
β-strand	82-83	2	5
β-strand	86-91	6	6
α-helix	100-109	10
α-helix	111-119	9
β-strand	125	1	6
β-strand	128-132	5	6
β-strand	140-145	6	6
α-helix	155-174	20
β-strand	179-182	4	6
α-helix	188-190	3
α-helix	194-212	19
α-helix	213-215	3
β-strand	218-223	6	6
α-helix	226-239	14

Chain D: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	23-27	5
β-strand	35-36	2	7
α-helix	37-39	3
α-helix	43-47	5
α-helix	68-70	3
β-strand	72-76	5	8
α-helix	79-81	3
β-strand	82-83	2	7
β-strand	86-91	6	8
α-helix	100-109	10
α-helix	111-118	8
β-strand	125	1	8
β-strand	128-132	5	8
β-strand	140-145	6	8
α-helix	155-174	20
β-strand	179-182	4	8
α-helix	188-190	3
α-helix	194-212	19
α-helix	213-215	3
β-strand	218-223	6	8
α-helix	226-239	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thioredoxin 1,ADP-ribose glycohydrolase MACROD2	A, B, C, D	protein	366	Escherichia coli (strain K12), Homo sapiens	A1Z1Q3 (AlphaFold model), P0AA25 (AlphaFold model)

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

>6Y4Z_1 Thioredoxin 1,ADP-ribose glycohydrolase MACROD2 (chains A, B, C, D)
MHHHHHHSSGMSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEY
QGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAG
TENLYFQSMKKKVWREEKERLLKMTLEERRKEYLRDYIPLNSILSWKEEMKGKGQNDEEN
TQETSQVKKSLTEKVSLYRGDITLLEVDAIVNAANASLLGGGGVDGCIHRAAGPCLLAEC
RNLNGCDTGHAKITCGYDLPAKYVIHTVGPIARGHINGSHKEDLANCYKSSLKLVKENNI
RSVAFPCISTGIYGFPNEPAAVIALNTIKEWLAKNHHEVDRIIFCVFLEVDFKIYKKKMN
EFFSVD

Ligands and cofactors

ID	Name	Formula	Copies
TLA	L(+)-tartaric acid	C4 H6 O6	1

Primary citation

Multiple crystal forms of human MacroD2. Wazir, S., Maksimainen, M.M., Lehtio, L. Acta Crystallogr F Struct Biol Commun (2020) 76:477-482. DOI 10.1107/S2053230X20011309 · PubMed

Other PDB entries of the same protein (UniProt A1Z1Q3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IQY 1.55 Å, Crystal structure of the human protein-proximal ADP-ribosyl-hydrolase MacroD2
6Y73 1.7 Å, The crystal structure of human MACROD2 in space group P43
6Y4Y 1.75 Å, The crystal structure of human MACROD2 in space group P41212

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