SMTL ID : 6wgs.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

3 x B12: COBALAMIN(Non-covalent)

B12.1: 28 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 17 PLIP interactions: 6 interactions with chain B, 11 interactions with chain A, Hydrophobic interactions: B:Y.39, B:Y.39, B:D.43, A:L.117, A:F.120, A:F.120, A:F.173, A:F.173, A:W.187 Hydrogen bonds: B:S.24, B:F.74, B:G.77, A:V.121, A:V.121, A:R.136, A:S.169 Water bridges: A:R.136 B12.3: 28 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.4 17 PLIP interactions: 6 interactions with chain C, 11 interactions with chain B, Hydrophobic interactions: C:Y.39, C:Y.39, C:D.43, B:L.117, B:F.120, B:F.120, B:F.173, B:F.173, B:W.187 Hydrogen bonds: C:S.24, C:F.74, C:G.77, B:V.121, B:V.121, B:R.136, B:S.169 Water bridges: B:R.136 B12.5: 28 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.6 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain A, Hydrophobic interactions: C:L.117, C:F.120, C:F.120, C:F.173, C:F.173, C:W.187, A:Y.39, A:Y.39, A:D.43 Hydrogen bonds: C:V.121, C:V.121, C:R.136, C:S.169, A:S.24, A:F.74, A:G.77 Water bridges: C:R.136

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

5AD.2: 10 residues within 4Å: Chain A: R.140, E.143, R.144 Chain B: T.21, G.22, K.31, L.36, Y.39, A.40 Ligands: B12.1 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:T.21, B:K.31, B:Y.39, A:R.140, A:R.140, A:R.140, A:R.144 Water bridges: B:G.22, A:R.140, A:R.140, A:R.140 pi-Cation interactions: A:R.140, A:R.140 5AD.4: 10 residues within 4Å: Chain B: R.140, E.143, R.144 Chain C: T.21, G.22, K.31, L.36, Y.39, A.40 Ligands: B12.3 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.140, B:R.140, B:R.140, B:R.144, C:T.21, C:K.31, C:Y.39 Water bridges: B:R.140, B:R.140, B:R.140, C:G.22 pi-Cation interactions: B:R.140, B:R.140 5AD.6: 10 residues within 4Å: Chain A: T.21, G.22, K.31, L.36, Y.39, A.40 Chain C: R.140, E.143, R.144 Ligands: B12.5 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.140, C:R.140, C:R.140, C:R.144, A:T.21, A:K.31, A:Y.39 Water bridges: C:R.140, C:R.140, C:R.140, A:G.22 pi-Cation interactions: C:R.140, C:R.140

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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