SMTL ID : 7rut.1 (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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: I.4 Ligands: ATP.3, K.6 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: K.24 Chain B: N.160 Ligands: ATP.3, K.6 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: K.24 Chain C: N.160 Ligands: ATP.9, K.13 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: N.160 Chain C: K.24 Ligands: ATP.14 No protein-ligand interaction detected (PLIP)

6 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: E.30, T.34, R.137, R.141 Chain B: R.137 Ligands: K.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.30 K.6: 5 residues within 4Å: Chain A: I.4 Chain B: D.164 Ligands: MG.1, ATP.3, MG.4 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.7: 4 residues within 4Å: Chain A: R.141 Chain B: R.141 Chain C: R.141 Ligands: K.2 No protein-ligand interaction detected (PLIP) K.8: 2 residues within 4Å: Chain B: K.123 Chain C: K.123 No protein-ligand interaction detected (PLIP) K.12: 4 residues within 4Å: Chain A: D.164 Chain C: I.4 Ligands: GOL.10, ATP.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:D.164, A:D.164, C:I.4 K.13: 4 residues within 4Å: Chain B: I.4 Chain C: D.164 Ligands: MG.5, ATP.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:I.4, C:D.164, C:D.164

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

ATP.3: 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.1, MG.4, K.6 18 PLIP interactions: 5 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:C.136, B:R.140, B:N.160, A:I.4, 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, A:T.6, A:T.6, A:S.15, A:S.15 Salt bridges: A:K.24, A:K.24 ATP.9: 19 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.5, K.13 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:I.4, B:T.6, B:K.7, B:T.8, B:G.9, B:F.13, B:S.14, B:S.15, B:K.24, C:C.136, C:R.140, C:N.160 Water bridges: B:I.4, B:T.6, B:T.6, B:S.15, B:S.15, C:N.160, C:R.161 Salt bridges: B:K.24, B:K.24 ATP.14: 21 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, D.10, F.13, S.14, S.15, K.24, F.29, G.33 Ligands: GOL.10, MG.11, K.12 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:T.6, 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, A:N.160, A:S.163 Salt bridges: C:K.24, C:K.24

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: S.163, D.164, F.167 Chain C: I.4 Ligands: K.12, ATP.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.164 Water bridges: A:S.163, C:I.4

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
E

B
D

C
A

Corrinoid adenosyltransferase

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