SMTL ID : 8d32.1

Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to 5-deoxyadenosylrhodibalamin and PPPi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x SF0: [5-(5,6-dimethyl-1H-benzimidazol-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl 1-{3-[3,14,19-tris(2-amino-2-oxoethyl)-8,13,18-tris(3-amino-3-oxopropyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1~2,5~.1~7,10~.1~12,15~]tricosa-5(23),6,10,12(21),15,17(20)-hexaen-4-yl-kappa~4~N~20~,N~21~,N~22~,N~23~]propanamido}propan-2-yl hydrogenato phosphate]rhodium (non-preferred name)(Non-covalent)

SF0.1: 39 residues within 4Å: Chain A: F.117, V.118, P.120, H.130, R.133, R.137, S.166, D.167, F.170, W.184, P.186, G.187 Chain C: V.3, H.4, L.5, T.6, R.7, I.8, T.10, T.12, G.19, L.20, S.21, M.23, Y.36, A.37, D.40, L.70, F.71, G.74, A.75, S.78, T.79, P.88, P.89, L.90 Ligands: 5AD.2, 3PO.3, MG.5 29 PLIP interactions: 18 interactions with chain C, 11 interactions with chain A, Hydrophobic interactions: C:V.3, C:Y.36, C:Y.36, C:D.40, C:A.75, C:L.90, C:L.90, A:F.117, A:F.117, A:F.117, A:F.170, A:F.170 Hydrogen bonds: C:V.3, C:V.3, C:T.6, C:T.6, C:R.7, C:I.8, C:S.21, C:L.70, C:G.74, C:A.75, C:L.90, A:V.118, A:V.118, A:R.133, A:R.137 Water bridges: A:R.133, A:D.167 SF0.6: 39 residues within 4Å: Chain A: V.3, H.4, L.5, T.6, R.7, I.8, T.10, T.12, G.19, L.20, S.21, M.23, Y.36, A.37, D.40, L.70, F.71, G.74, A.75, S.78, T.79, P.88, P.89, L.90 Chain B: F.117, V.118, P.120, H.130, R.133, R.137, S.166, D.167, F.170, W.184, P.186, G.187 Ligands: 5AD.7, 3PO.8, MG.10 29 PLIP interactions: 18 interactions with chain A, 11 interactions with chain B, Hydrophobic interactions: A:V.3, A:Y.36, A:Y.36, A:D.40, A:A.75, A:L.90, A:L.90, B:F.117, B:F.117, B:F.117, B:F.170, B:F.170 Hydrogen bonds: A:V.3, A:V.3, A:T.6, A:T.6, A:R.7, A:I.8, A:S.21, A:L.70, A:G.74, A:A.75, A:L.90, B:V.118, B:V.118, B:R.133, B:R.137 Water bridges: B:R.133, B:D.167 SF0.11: 39 residues within 4Å: Chain B: V.3, H.4, L.5, T.6, R.7, I.8, T.10, T.12, G.19, L.20, S.21, M.23, Y.36, A.37, D.40, L.70, F.71, G.74, A.75, S.78, T.79, P.88, P.89, L.90 Chain C: F.117, V.118, P.120, H.130, R.133, R.137, S.166, D.167, F.170, W.184, P.186, G.187 Ligands: 5AD.12, 3PO.13, MG.15 29 PLIP interactions: 11 interactions with chain C, 18 interactions with chain B, Hydrophobic interactions: C:F.117, C:F.117, C:F.117, C:F.170, C:F.170, B:V.3, B:Y.36, B:Y.36, B:D.40, B:A.75, B:L.90, B:L.90 Hydrogen bonds: C:V.118, C:V.118, C:R.133, C:R.137, B:V.3, B:V.3, B:T.6, B:T.6, B:R.7, B:I.8, B:S.21, B:L.70, B:G.74, B:A.75, B:L.90 Water bridges: C:R.133, C:D.167

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

5AD.2: 11 residues within 4Å: Chain A: R.137, E.140, R.141 Chain C: T.18, G.19, K.28, L.33, Y.36, A.37 Ligands: SF0.1, 3PO.3 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:R.137, A:R.137, A:R.141, C:T.18, C:Y.36, C:Y.36 Water bridges: A:R.137, A:R.137, A:R.137, C:G.19 pi-Cation interactions: A:R.137, A:R.137 5AD.7: 11 residues within 4Å: Chain A: T.18, G.19, K.28, L.33, Y.36, A.37 Chain B: R.137, E.140, R.141 Ligands: SF0.6, 3PO.8 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:T.18, A:Y.36, A:Y.36, B:R.137, B:R.137, B:R.141 Water bridges: A:G.19, B:R.137, B:R.137, B:R.137 pi-Cation interactions: B:R.137, B:R.137 5AD.12: 11 residues within 4Å: Chain B: T.18, G.19, K.28, L.33, Y.36, A.37 Chain C: R.137, E.140, R.141 Ligands: SF0.11, 3PO.13 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:T.18, B:Y.36, B:Y.36, C:R.137, C:R.137, C:R.141 Water bridges: B:G.19, C:R.137, C:R.137, C:R.137 pi-Cation interactions: C:R.137, C:R.137

3 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.3: 17 residues within 4Å: Chain A: R.137, N.163, R.164, D.167 Chain C: Y.9, T.10, R.11, T.12, G.13, D.14, T.17, T.18, K.28 Ligands: SF0.1, 5AD.2, MG.4, MG.5 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain C Hydrogen bonds: A:N.163, A:D.167, C:T.10, C:R.11, C:T.12, C:T.12, C:G.13, C:T.18 Water bridges: A:R.137, A:R.137, A:R.137, A:R.164, C:G.19, C:R.25 Salt bridges: A:R.137, C:K.28, C:K.28 3PO.8: 17 residues within 4Å: Chain A: Y.9, T.10, R.11, T.12, G.13, D.14, T.17, T.18, K.28 Chain B: R.137, N.163, R.164, D.167 Ligands: SF0.6, 5AD.7, MG.9, MG.10 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:T.10, A:R.11, A:T.12, A:T.12, A:G.13, A:T.18, B:N.163, B:D.167 Water bridges: A:G.19, A:R.25, B:R.137, B:R.137, B:R.137, B:R.164 Salt bridges: A:K.28, A:K.28, B:R.137 3PO.13: 17 residues within 4Å: Chain B: Y.9, T.10, R.11, T.12, G.13, D.14, T.17, T.18, K.28 Chain C: R.137, N.163, R.164, D.167 Ligands: SF0.11, 5AD.12, MG.14, MG.15 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:T.10, B:R.11, B:T.12, B:T.12, B:G.13, B:T.18, C:N.163, C:D.167 Water bridges: B:G.19, B:R.25, C:R.137, C:R.137, C:R.137, C:R.164 Salt bridges: B:K.28, B:K.28, C:R.137

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: R.137, N.163 Chain C: K.28 Ligands: 3PO.3, MG.5 No protein-ligand interaction detected (PLIP) MG.5: 7 residues within 4Å: Chain A: D.167 Chain C: I.8, Y.9, T.10 Ligands: SF0.1, 3PO.3, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:D.167, A:D.167, C:I.8 MG.9: 5 residues within 4Å: Chain A: K.28 Chain B: R.137, N.163 Ligands: 3PO.8, MG.10 No protein-ligand interaction detected (PLIP) MG.10: 7 residues within 4Å: Chain A: I.8, Y.9, T.10 Chain B: D.167 Ligands: SF0.6, 3PO.8, MG.9 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:I.8, B:D.167, B:D.167 MG.14: 5 residues within 4Å: Chain B: K.28 Chain C: R.137, N.163 Ligands: 3PO.13, MG.15 No protein-ligand interaction detected (PLIP) MG.15: 7 residues within 4Å: Chain B: I.8, Y.9, T.10 Chain C: D.167 Ligands: SF0.11, 3PO.13, MG.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:I.8, C:D.167, C:D.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruetz, M. et al., A Noble Metal Substitution Leads to B 12 Cofactor Mimicry by a Rhodibalamin. Biochemistry (2024)

Release Date

2023-05-10

Peptides

Corrinoid adenosyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Corrinoid adenosyltransferase

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