SMTL ID : 7ruv.1 (1 other biounit)

Structure of Human ATP:Cobalamin Adenosyltransferase E193K bound to adenosylcobalamin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 8 residues within 4Å: Chain A: R.137, R.141 Chain B: R.137, R.141 Chain C: R.137, R.141 Ligands: K.5, K.9 No protein-ligand interaction detected (PLIP) K.5: 8 residues within 4Å: Chain A: R.137, R.141 Chain B: R.137, R.141 Chain C: R.137, R.141 Ligands: K.1, K.9 No protein-ligand interaction detected (PLIP) K.9: 8 residues within 4Å: Chain A: R.137, R.141 Chain B: R.137, R.141 Chain C: R.137, R.141 Ligands: K.1, K.5 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 2 residues within 4Å: Ligands: MG.6, MG.10 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Ligands: MG.2, MG.10 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Ligands: MG.2, MG.6 No protein-ligand interaction detected (PLIP)

3 x B12: COBALAMIN(Non-covalent)

B12.3: 17 residues within 4Å: Chain A: L.113, T.114, A.115, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Chain C: V.32, D.36, Q.68, G.71, S.72, A.75 Ligands: 5AD.4 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain C, Hydrophobic interactions: A:L.113, A:F.167, A:F.167, C:V.32, C:V.32, C:D.36, C:A.75 Hydrogen bonds: A:I.117, A:I.117, A:R.132, A:R.136, A:S.163, A:D.164, C:Q.68 Water bridges: A:F.116 B12.7: 17 residues within 4Å: Chain A: V.32, D.36, Q.68, G.71, S.72, A.75 Chain B: L.113, T.114, A.115, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Ligands: 5AD.8 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B, Hydrophobic interactions: A:V.32, A:V.32, A:D.36, A:A.75, B:L.113, B:F.167, B:F.167 Hydrogen bonds: A:Q.68, B:I.117, B:I.117, B:R.132, B:R.136, B:S.163, B:D.164 Water bridges: B:F.116 B12.11: 17 residues within 4Å: Chain B: V.32, D.36, Q.68, G.71, S.72, A.75 Chain C: L.113, T.114, A.115, F.116, I.117, R.132, R.136, S.163, D.164, F.167 Ligands: 5AD.12 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:L.113, C:F.167, C:F.167, B:V.32, B:V.32, B:D.36, B:A.75 Hydrogen bonds: C:I.117, C:I.117, C:R.132, C:R.136, C:S.163, C:D.164, B:Q.68 Water bridges: C:F.116

3 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.4: 5 residues within 4Å: Chain A: R.136, K.139, R.140 Chain C: F.29 Ligands: B12.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.136, A:R.136, A:R.140 Water bridges: A:R.136, A:K.139, A:K.139 pi-Cation interactions: A:R.136, A:R.136 pi-Stacking: C:F.29 5AD.8: 5 residues within 4Å: Chain A: F.29 Chain B: R.136, K.139, R.140 Ligands: B12.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.136, B:R.136, B:R.140 Water bridges: B:R.136, B:K.139, B:K.139 pi-Cation interactions: B:R.136, B:R.136 pi-Stacking: A:F.29 5AD.12: 5 residues within 4Å: Chain B: F.29 Chain C: R.136, K.139, R.140 Ligands: B12.11 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.136, C:R.136, C:R.140 Water bridges: C:R.136, C:K.139, C:K.139 pi-Cation interactions: C:R.136, C:R.136 pi-Stacking: B:F.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gouda, H. et al., Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions. J.Biol.Chem. (2021)

Release Date

2021-11-24

Peptides

Corrinoid adenosyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Corrinoid adenosyltransferase

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