SMTL ID : 6wh5.1

Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to cob(II)alamin and PPPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-trimer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 7 residues within 4Å: Chain A: D.170 Chain C: I.11, Y.12, T.13 Ligands: MG.2, 3PO.10, B12.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:D.170, A:D.170, C:I.11 K.5: 7 residues within 4Å: Chain A: I.11, Y.12, T.13 Chain B: D.170 Ligands: 3PO.3, B12.4, MG.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.170, B:D.170, A:I.11 K.8: 7 residues within 4Å: Chain B: I.11, Y.12, T.13 Chain C: D.170 Ligands: 3PO.7, MG.9, B12.11 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.170, C:D.170, B:I.11

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: R.140, N.166 Chain C: K.31 Ligands: K.1, 3PO.10 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: K.31 Chain B: R.140, N.166 Ligands: 3PO.3, K.5 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain B: K.31 Chain C: R.140, N.166 Ligands: 3PO.7, K.8 No protein-ligand interaction detected (PLIP)

3 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.3: 15 residues within 4Å: Chain A: Y.12, T.13, R.14, T.15, G.16, D.17, T.20, T.21, K.31 Chain B: R.140, N.166, D.170 Ligands: B12.4, K.5, MG.6 21 PLIP interactions: 12 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:T.13, A:T.13, A:R.14, A:T.15, A:T.15, A:G.16, A:T.20, A:T.21, B:N.166 Water bridges: A:R.28, A:K.31, B:R.140, B:R.140, B:R.140, B:R.140, B:R.140, B:N.166, B:R.167 Salt bridges: A:K.31, A:K.31, B:R.140 3PO.7: 16 residues within 4Å: Chain B: I.11, Y.12, T.13, R.14, T.15, G.16, D.17, T.20, T.21, K.31 Chain C: R.140, N.166, D.170 Ligands: K.8, MG.9, B12.11 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:T.13, B:T.13, B:R.14, B:T.15, B:G.16, B:T.21, B:T.21, C:N.166, C:N.166 Water bridges: B:R.28, C:R.140, C:R.140, C:R.140, C:R.140, C:R.140, C:N.166, C:R.167 Salt bridges: B:K.31, B:K.31, C:R.140 3PO.10: 16 residues within 4Å: Chain A: R.140, N.166, D.170 Chain C: I.11, Y.12, T.13, R.14, T.15, G.16, D.17, T.20, T.21, K.31 Ligands: K.1, MG.2, B12.12 21 PLIP interactions: 10 interactions with chain A, 11 interactions with chain C Hydrogen bonds: A:N.166, A:N.166, C:I.11, C:T.13, C:T.13, C:R.14, C:T.15, C:G.16, C:T.21, C:T.21 Water bridges: A:R.140, A:R.140, A:R.140, A:R.140, A:R.140, A:R.140, A:R.167, C:R.28 Salt bridges: A:R.140, C:K.31, C:K.31

3 x B12: COBALAMIN(Non-covalent)

B12.4: 39 residues within 4Å: Chain A: V.6, H.7, L.8, T.9, R.10, I.11, T.13, T.15, G.22, L.23, S.24, M.26, Y.39, A.40, D.43, F.74, G.77, A.78, S.81, T.82, H.90, P.91, P.92, L.93, R.94 Chain B: F.120, V.121, P.123, H.133, R.136, R.140, S.169, D.170, F.173, W.187, P.189, G.190 Ligands: 3PO.3, K.5 27 PLIP interactions: 16 interactions with chain A, 11 interactions with chain B, Hydrophobic interactions: A:I.11, A:T.13, A:Y.39, A:Y.39, A:F.74, A:L.93, A:L.93, B:F.120, B:F.120, B:F.120, B:F.173, B:F.173 Hydrogen bonds: A:T.9, A:T.9, A:I.11, A:T.13, A:T.13, A:S.24, A:F.74, A:G.77, A:L.93, B:V.121, B:V.121, B:R.136, B:R.140, B:S.169 Water bridges: B:R.136 B12.11: 39 residues within 4Å: Chain B: V.6, H.7, L.8, T.9, R.10, I.11, T.13, T.15, G.22, L.23, S.24, M.26, Y.39, A.40, D.43, F.74, G.77, A.78, S.81, T.82, H.90, P.91, P.92, L.93, R.94 Chain C: F.120, V.121, P.123, H.133, R.136, R.140, S.169, D.170, F.173, W.187, P.189, G.190 Ligands: 3PO.7, K.8 28 PLIP interactions: 19 interactions with chain B, 9 interactions with chain C, Hydrophobic interactions: B:V.6, B:I.11, B:T.13, B:Y.39, B:Y.39, B:D.43, B:F.74, B:L.93, B:L.93, C:F.120, C:F.120, C:F.173, C:F.173 Hydrogen bonds: B:T.9, B:T.9, B:R.10, B:I.11, B:T.13, B:T.13, B:S.24, B:F.74, B:G.77, B:L.93, C:V.121, C:V.121, C:R.136, C:R.140, C:S.169 B12.12: 39 residues within 4Å: Chain A: F.120, V.121, P.123, H.133, R.136, R.140, S.169, D.170, F.173, W.187, P.189, G.190 Chain C: V.6, H.7, L.8, T.9, R.10, I.11, T.13, T.15, G.22, L.23, S.24, M.26, Y.39, A.40, D.43, F.74, G.77, A.78, S.81, T.82, H.90, P.91, P.92, L.93, R.94 Ligands: K.1, 3PO.10 31 PLIP interactions: 20 interactions with chain C, 11 interactions with chain A, Hydrophobic interactions: C:V.6, C:V.6, C:T.13, C:Y.39, C:Y.39, C:D.43, C:F.74, C:A.78, C:L.93, C:L.93, A:F.120, A:F.120, A:F.120, A:F.120, A:F.173, A:F.173 Hydrogen bonds: C:T.9, C:T.9, C:I.11, C:T.13, C:T.13, C:L.23, C:F.74, C:G.77, C:L.93, A:V.121, A:V.121, A:R.136, A:R.140, A:S.169 Water bridges: C:R.10

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
B

C
C

Corrinoid adenosyltransferase

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