SMTL ID : 6wgv.1

Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to adenosylcobalamin and PPPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-trimer

Ligands

3 x B12: COBALAMIN(Non-covalent)

B12.1: 29 residues within 4Å: Chain A: L.117, K.118, S.119, F.120, V.121, P.123, H.133, R.136, R.140, S.169, D.170, F.173, W.187, P.189 Chain B: G.22, L.23, S.24, M.26, Y.39, A.40, D.43, L.73, F.74, G.77, A.78, S.81, L.93 Ligands: 5AD.2, 3PO.3 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:L.117, A:F.120, A:F.173, A:F.173, A:F.173, A:W.187, B:Y.39, B:Y.39, B:D.43 Hydrogen bonds: A:V.121, A:V.121, A:R.136, A:R.140, A:S.169, B:S.24, B:F.74, B:G.77 B12.5: 29 residues within 4Å: Chain B: L.117, K.118, S.119, F.120, V.121, P.123, H.133, R.136, R.140, S.169, D.170, F.173, W.187, P.189 Chain C: G.22, L.23, S.24, M.26, Y.39, A.40, D.43, L.73, F.74, G.77, A.78, S.81, L.93 Ligands: 5AD.6, 3PO.7 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain C, Hydrophobic interactions: B:L.117, B:F.120, B:F.173, B:F.173, B:F.173, B:W.187, C:Y.39, C:Y.39, C:D.43 Hydrogen bonds: B:V.121, B:V.121, B:R.136, B:R.140, B:S.169, C:S.24, C:F.74, C:G.77 B12.9: 29 residues within 4Å: Chain A: G.22, L.23, S.24, M.26, Y.39, A.40, D.43, L.73, F.74, G.77, A.78, S.81, L.93 Chain C: L.117, K.118, S.119, F.120, V.121, P.123, H.133, R.136, R.140, S.169, D.170, F.173, W.187, P.189 Ligands: 5AD.10, 3PO.11 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain C, Hydrophobic interactions: A:Y.39, A:Y.39, A:D.43, C:L.117, C:F.120, C:F.173, C:F.173, C:F.173, C:W.187 Hydrogen bonds: A:S.24, A:F.74, A:G.77, C:V.121, C:V.121, C:R.136, C:R.140, C:S.169

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

5AD.2: 12 residues within 4Å: Chain A: R.140, E.143, R.144 Chain B: T.21, G.22, L.23, K.31, L.36, Y.39, A.40 Ligands: B12.1, 3PO.3 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.140, A:E.143, A:R.144, B:G.22, B:Y.39 Water bridges: A:R.140, A:R.140 pi-Cation interactions: A:R.140, A:R.140 5AD.6: 12 residues within 4Å: Chain B: R.140, E.143, R.144 Chain C: T.21, G.22, L.23, K.31, L.36, Y.39, A.40 Ligands: B12.5, 3PO.7 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.140, B:E.143, B:R.144, C:G.22, C:Y.39 Water bridges: B:R.140, B:R.140 pi-Cation interactions: B:R.140, B:R.140 5AD.10: 12 residues within 4Å: Chain A: T.21, G.22, L.23, K.31, L.36, Y.39, A.40 Chain C: R.140, E.143, R.144 Ligands: B12.9, 3PO.11 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:G.22, A:Y.39, C:R.140, C:E.143, C:R.144 Water bridges: C:R.140, C:R.140 pi-Cation interactions: C:R.140, C:R.140

3 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.3: 8 residues within 4Å: Chain A: R.140, N.166, D.170 Chain B: T.21, K.31 Ligands: B12.1, 5AD.2, MG.4 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.166, A:N.166, B:T.21, B:T.21 Water bridges: A:R.140, A:R.140, A:R.140 Salt bridges: A:R.140, B:K.31 3PO.7: 8 residues within 4Å: Chain B: R.140, N.166, D.170 Chain C: T.21, K.31 Ligands: B12.5, 5AD.6, MG.8 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:T.21, C:T.21, B:N.166, B:N.166 Salt bridges: C:K.31, B:R.140 Water bridges: B:R.140, B:R.140, B:R.140 3PO.11: 8 residues within 4Å: Chain A: T.21, K.31 Chain C: R.140, N.166, D.170 Ligands: B12.9, 5AD.10, MG.12 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:T.21, A:T.21, C:N.166, C:N.166 Salt bridges: A:K.31, C:R.140 Water bridges: C:R.140, C:R.140, C:R.140

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: R.140, N.166 Chain B: K.31 Ligands: 3PO.3 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: R.140, N.166 Chain C: K.31 Ligands: 3PO.7 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain A: K.31 Chain C: R.140, N.166 Ligands: 3PO.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mascarenhas, R. et al., Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B 12 . Proc.Natl.Acad.Sci.USA (2020)

Release Date

2021-01-20

Peptides

Corrinoid adenosyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Corrinoid adenosyltransferase

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