SMTL ID : 7ruu.2 (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

4 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.63, A:F.158 Salt bridges: A:K.62 ACT.5: 7 residues within 4Å: Chain B: K.62, I.63, T.66, P.95, E.98, W.102, F.158 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.95 Hydrogen bonds: B:T.66, B:T.66, B:E.98 ACT.8: 4 residues within 4Å: Chain A: R.141 Chain B: R.141 Chain C: E.30, R.141 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Salt bridges: C:R.141, B:R.141, A:R.141 ACT.9: 8 residues within 4Å: Chain C: K.62, I.63, T.66, P.95, E.98, L.99, W.102, F.158 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:E.98, C:L.99, C:W.102 Hydrogen bonds: C:T.66, C:E.98

1 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: R.137, R.141 Chain B: R.141 Chain C: R.141 No protein-ligand interaction detected (PLIP)

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

5AD.3: 5 residues within 4Å: Chain A: C.136, E.139, R.140 Chain B: F.29 Ligands: B12.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.136, A:R.140 5AD.6: 5 residues within 4Å: Chain B: C.136, E.139, R.140 Chain C: F.29 Ligands: B12.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.136, B:R.140 Water bridges: B:N.160 5AD.10: 5 residues within 4Å: Chain A: F.29 Chain C: C.136, E.139, R.140 Ligands: B12.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:C.136, C:E.139, C:R.140 Water bridges: C:N.160

3 x B12: COBALAMIN(Non-covalent)

B12.4: 16 residues within 4Å: Chain A: L.113, T.114, A.115, F.116, I.117, R.132, S.163, D.164, F.167 Chain B: V.32, D.36, Q.68, G.71, S.72, A.75 Ligands: 5AD.3 17 PLIP interactions: 8 interactions with chain B, 9 interactions with chain A, Hydrophobic interactions: B:V.32, B:D.36, B:A.75, A:L.113, A:F.167, A:F.167 Hydrogen bonds: B:Q.68, A:I.117, A:I.117, A:R.132, A:S.163 Water bridges: B:D.36, B:Q.68, B:Q.68, B:S.72, A:F.116, A:R.132 B12.7: 17 residues within 4Å: Chain B: L.113, T.114, A.115, F.116, I.117, R.132, S.163, D.164, F.167 Chain C: V.32, D.36, Q.68, G.71, S.72, A.75, T.76 Ligands: 5AD.6 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain C, Hydrophobic interactions: B:L.113, B:F.116, B:F.167, B:F.167, C:V.32, C:D.36, C:A.75 Hydrogen bonds: B:I.117, B:I.117, B:R.132, B:S.163, C:Q.68, C:S.72 Water bridges: B:F.116, B:R.132, C:D.36, C:G.71 B12.11: 15 residues within 4Å: Chain A: 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.10 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain A, Hydrophobic interactions: C:L.113, C:F.167, C:F.167, A:D.36, A:A.75 Hydrogen bonds: C:I.117, C:I.117, C:R.132, C:S.163, C:D.164, A:Q.68 Water bridges: C:F.116, C:R.132, A:Q.68, A:G.71

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
C

B
D

C
B

Corrinoid adenosyltransferase

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