SMTL ID : 9dxu.1

Crystal structure of cobalt-incorporated human 2-aminoethanethiol (aka cysteamine) dioxygenase (ADO) variant C18S/C239S in complex with CP6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 11 residues within 4Å: Chain A: F.102, H.113, H.115, H.194, I.196, D.207, L.209, Y.213 Chain B: W.8, L.9 Ligands: CO.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.8, A:Y.213

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: N.68, P.265 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.68 GOL.3: 5 residues within 4Å: Chain A: S.173, Y.177, C.184, I.185, D.191 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.173, A:S.173, A:I.185, A:D.191 Water bridges: A:D.191 GOL.4: 6 residues within 4Å: Chain A: P.85, G.107, T.108, S.109, D.256, F.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.109, A:S.109 Water bridges: A:D.256, A:D.256

10 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.5: 2 residues within 4Å: Chain A: E.50, S.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.53 SCN.6: 3 residues within 4Å: Chain A: Q.77, P.78, P.80 No protein-ligand interaction detected (PLIP) SCN.7: 1 residues within 4Å: Chain A: L.137 No protein-ligand interaction detected (PLIP) SCN.8: 4 residues within 4Å: Chain A: F.154, P.157, L.158, R.163 No protein-ligand interaction detected (PLIP) SCN.9: 4 residues within 4Å: Chain A: A.8, S.9, Q.12, K.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.9 SCN.10: 1 residues within 4Å: Chain A: H.189 No protein-ligand interaction detected (PLIP) SCN.11: 6 residues within 4Å: Chain A: D.135, K.136, P.188, H.189, N.192, L.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.135 SCN.12: 1 residues within 4Å: Chain A: D.216 No protein-ligand interaction detected (PLIP) SCN.13: 4 residues within 4Å: Chain A: P.157, Q.159, E.162, R.225 No protein-ligand interaction detected (PLIP) SCN.15: 4 residues within 4Å: Chain B: X.1, Y.2, I.3, R.13 No protein-ligand interaction detected (PLIP)

1 x CO: COBALT (II) ION(Non-covalent)

CO.14: 4 residues within 4Å: Chain A: H.113, H.115, H.194 Ligands: TRS.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.113, A:H.115, A:H.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiramongkol, Y. et al., An mRNA-display derived cyclic peptide scaffold reveals the substrate binding interactions of an N-terminal cysteine oxidase. Nat Commun (2025)

Release Date

2025-06-04

Peptides

2-aminoethanethiol dioxygenase: A
CP6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-aminoethanethiol dioxygenase

CP6

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