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

Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound to adenosylcobalamin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: K.62, I.63, T.66, P.95, E.98, L.99, W.102, F.158 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.63, A:F.158 Hydrogen bonds: A:T.66 Salt bridges: A:K.62 ACT.6: 8 residues within 4Å: Chain B: K.62, I.63, T.66, P.95, E.98, L.99, W.102, F.158 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.63, B:F.158 Hydrogen bonds: B:T.66 Salt bridges: B:K.62 ACT.11: 8 residues within 4Å: Chain C: K.62, I.63, T.66, P.95, E.98, L.99, W.102, F.158 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.63, C:F.158 Hydrogen bonds: C:T.66 Salt bridges: C:K.62

6 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: R.141 Chain B: R.141 Chain C: R.141 Ligands: K.7, K.12 No protein-ligand interaction detected (PLIP) K.3: 5 residues within 4Å: Chain A: K.123 Chain B: K.123 Chain C: K.123 Ligands: K.8, K.13 No protein-ligand interaction detected (PLIP) K.7: 5 residues within 4Å: Chain A: R.141 Chain B: R.141 Chain C: R.141 Ligands: K.2, K.12 No protein-ligand interaction detected (PLIP) K.8: 5 residues within 4Å: Chain A: K.123 Chain B: K.123 Chain C: K.123 Ligands: K.3, K.13 No protein-ligand interaction detected (PLIP) K.12: 5 residues within 4Å: Chain A: R.141 Chain B: R.141 Chain C: R.141 Ligands: K.2, K.7 No protein-ligand interaction detected (PLIP) K.13: 5 residues within 4Å: Chain A: K.123 Chain B: K.123 Chain C: K.123 Ligands: K.3, K.8 No protein-ligand interaction detected (PLIP)

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

5AD.4: 5 residues within 4Å: Chain A: C.136, E.139, R.140 Chain C: F.29 Ligands: B12.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.136, A:E.139, A:R.140 5AD.9: 5 residues within 4Å: Chain A: F.29 Chain B: C.136, E.139, R.140 Ligands: B12.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.136, B:E.139, B:R.140 5AD.14: 5 residues within 4Å: Chain B: F.29 Chain C: C.136, E.139, R.140 Ligands: B12.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:C.136, C:E.139, C:R.140

3 x B12: COBALAMIN(Non-covalent)

B12.5: 15 residues within 4Å: Chain A: L.113, T.114, A.115, F.116, I.117, R.132, S.163, D.164, F.167 Chain C: D.36, Q.68, G.71, S.72, A.75 Ligands: 5AD.4 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain A, Hydrophobic interactions: C:D.36, C:A.75, A:L.113, A:F.167, A:F.167 Hydrogen bonds: C:Q.68, A:I.117, A:I.117, A:R.132, A:S.163, A:D.164 Water bridges: C:G.71, A:F.116 B12.10: 15 residues within 4Å: Chain A: D.36, Q.68, G.71, S.72, A.75 Chain B: L.113, T.114, A.115, F.116, I.117, R.132, S.163, D.164, F.167 Ligands: 5AD.9 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B, Hydrophobic interactions: 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:S.163, B:D.164 Water bridges: A:G.71, B:F.116 B12.15: 15 residues within 4Å: Chain B: D.36, Q.68, G.71, S.72, A.75 Chain C: L.113, T.114, A.115, F.116, I.117, R.132, S.163, D.164, F.167 Ligands: 5AD.14 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain C, Hydrophobic interactions: B:D.36, B:A.75, C:L.113, C:F.167, C:F.167 Hydrogen bonds: B:Q.68, C:I.117, C:I.117, C:R.132, C:S.163, C:D.164 Water bridges: B:G.71, C:F.116

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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