SMTL ID : 7rut.2 (1 other biounit)

Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound to ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: N.160 Chain C: K.24 Ligands: K.3, ATP.13 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: I.4 Chain B: D.164 Ligands: ATP.5, K.8 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: K.24 Chain B: N.160 Ligands: ATP.5, K.8 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: I.4 Chain C: D.164 Ligands: ATP.9, K.11 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: K.24 Chain C: N.160 Ligands: ATP.9, K.11 No protein-ligand interaction detected (PLIP)

5 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: D.164 Chain C: I.4 Ligands: MG.1, ATP.13 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:D.164, A:D.164, C:I.4, H2O.13 K.4: 2 residues within 4Å: Chain A: K.123 Chain C: K.123 No protein-ligand interaction detected (PLIP) K.8: 5 residues within 4Å: Chain A: I.4 Chain B: D.164 Ligands: MG.2, ATP.5, MG.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:I.4, B:D.164, B:D.164 K.11: 5 residues within 4Å: Chain B: I.4 Chain C: D.164 Ligands: MG.7, ATP.9, MG.10 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.164, C:D.164, B:I.4 K.12: 4 residues within 4Å: Chain A: R.141 Chain B: R.141 Chain C: R.137, R.141 No protein-ligand interaction detected (PLIP)

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 20 residues within 4Å: Chain A: I.4, Y.5, T.6, K.7, T.8, G.9, F.13, S.14, S.15, K.24, F.29, G.33 Chain B: C.136, E.139, R.140, N.160, D.164 Ligands: MG.2, MG.6, K.8 18 PLIP interactions: 7 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:C.136, B:R.140, B:N.160, B:D.164, A:T.6, A:K.7, A:G.9, A:S.14, A:S.15, A:K.24 Water bridges: B:N.160, B:R.161, B:S.163, A:I.4, A:S.15, A:S.15 Salt bridges: A:K.24, A:K.24 ATP.9: 20 residues within 4Å: Chain B: I.4, Y.5, T.6, K.7, T.8, G.9, F.13, S.14, S.15, K.24, F.29, G.33 Chain C: C.136, E.139, R.140, N.160, D.164 Ligands: MG.7, MG.10, K.11 20 PLIP interactions: 5 interactions with chain C, 15 interactions with chain B Hydrogen bonds: C:C.136, C:R.140, C:N.160, B:I.4, B:T.6, B:K.7, B:T.8, B:G.9, B:S.15 Water bridges: C:N.160, C:R.161, B:I.4, B:T.6, B:T.6, B:S.15, B:S.15, B:K.24, B:K.24 Salt bridges: B:K.24, B:K.24 ATP.13: 18 residues within 4Å: Chain A: C.136, E.139, R.140, N.160, D.164 Chain C: I.4, Y.5, T.6, K.7, T.8, G.9, F.13, S.14, S.15, K.24, F.29 Ligands: MG.1, K.3 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:T.6, C:K.7, C:T.8, C:G.9, C:S.15, A:C.136, A:E.139, A:R.140, A:N.160, A:D.164 Water bridges: C:S.15, C:S.15, C:K.24, C:K.24, A:N.160, A:R.161 Salt bridges: C:K.24, C:K.24

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
F

C
B

Corrinoid adenosyltransferase

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