SMTL ID : 6b5k.1

Mycobacterium tuberculosis RmlA in complex with Mg/dTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 21 residues within 4Å: Chain A: L.6, A.7, G.8, G.9, S.10, G.11, T.12, R.13, K.23, Q.24, Q.80, P.83, D.84, G.85, L.86, L.106, G.107, D.108, E.193 Ligands: MG.2, MG.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.86 Hydrogen bonds: A:G.8, A:S.10, A:G.11, A:T.12, A:R.13, A:Q.80, A:Q.80, A:G.85, A:G.107, A:D.108, A:D.108 Water bridges: A:G.9, A:G.9, A:T.12, A:T.12, A:R.13, A:R.13, A:R.13, A:K.23, A:R.191, A:R.191 Salt bridges: A:R.13, A:R.13, A:K.23, A:K.23, A:K.23 TTP.8: 21 residues within 4Å: Chain B: L.6, A.7, G.8, G.9, S.10, G.11, T.12, R.13, K.23, Q.24, Q.80, P.83, D.84, G.85, L.86, L.106, G.107, D.108, E.193 Ligands: MG.6, MG.7 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.86 Hydrogen bonds: B:G.8, B:G.9, B:G.11, B:T.12, B:R.13, B:Q.80, B:Q.80, B:G.85, B:G.107, B:D.108, B:D.108 Water bridges: B:S.10, B:S.10, B:R.13, B:R.13, B:R.13, B:K.23 Salt bridges: B:R.13, B:R.13, B:K.23, B:K.23, B:K.23, D:K.274 TTP.10: 21 residues within 4Å: Chain C: L.6, A.7, G.8, G.9, S.10, G.11, T.12, R.13, K.23, Q.24, Q.80, P.83, D.84, G.85, L.86, L.106, G.107, D.108, E.193 Ligands: MG.11, MG.12 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:L.86 Hydrogen bonds: C:G.8, C:S.10, C:G.11, C:T.12, C:R.13, C:Q.80, C:Q.80, C:G.85, C:G.107, C:D.108, C:D.108 Water bridges: C:G.9, C:G.9, C:T.12, C:T.12, C:R.13, C:R.13, C:R.13, C:K.23, C:R.191, C:R.191 Salt bridges: C:R.13, C:R.13, C:K.23, C:K.23, C:K.23 TTP.17: 21 residues within 4Å: Chain D: L.6, A.7, G.8, G.9, S.10, G.11, T.12, R.13, K.23, Q.24, Q.80, P.83, D.84, G.85, L.86, L.106, G.107, D.108, E.193 Ligands: MG.15, MG.16 24 PLIP interactions: 23 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.86 Hydrogen bonds: D:G.8, D:G.9, D:G.11, D:T.12, D:R.13, D:Q.80, D:Q.80, D:G.85, D:G.107, D:D.108, D:D.108 Water bridges: D:S.10, D:S.10, D:R.13, D:R.13, D:R.13, D:K.23 Salt bridges: D:R.13, D:R.13, D:K.23, D:K.23, D:K.23, B:K.274

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: K.23, D.108, D.222 Ligands: TTP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.108, A:D.222, H2O.1, H2O.4, H2O.5 MG.3: 1 residues within 4Å: Ligands: TTP.1 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: TTP.8 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: K.23, D.108, D.222 Ligands: TTP.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.108, B:D.222, H2O.10, H2O.10, H2O.12 MG.11: 4 residues within 4Å: Chain C: K.23, D.108, D.222 Ligands: TTP.10 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.108, C:D.222, H2O.15, H2O.17, H2O.19 MG.12: 1 residues within 4Å: Ligands: TTP.10 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: TTP.17 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain D: K.23, D.108, D.222 Ligands: TTP.17 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.108, D:D.222, H2O.23, H2O.24, H2O.26

4 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.4: 15 residues within 4Å: Chain A: M.43, F.111, Y.112, G.113, P.114, G.115, L.116, G.117, T.118, S.119, V.247, S.248, E.252, V.253, R.256 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.113, A:G.113, A:G.115, A:G.117, A:T.118, A:T.118, A:S.119, A:S.119, A:S.248 Water bridges: A:Y.112, A:I.249, A:E.252 TYD.9: 15 residues within 4Å: Chain B: M.43, F.111, Y.112, G.113, P.114, G.115, L.116, G.117, T.118, S.119, V.247, S.248, E.252, V.253, R.256 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.113, B:G.113, B:G.115, B:G.117, B:T.118, B:T.118, B:T.118, B:S.119, B:S.248 Water bridges: B:I.249, B:I.249 TYD.13: 15 residues within 4Å: Chain C: M.43, F.111, Y.112, G.113, P.114, G.115, L.116, G.117, T.118, S.119, V.247, S.248, E.252, V.253, R.256 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.113, C:G.113, C:G.115, C:G.117, C:T.118, C:T.118, C:S.119, C:S.119, C:S.248 Water bridges: C:Y.112, C:I.249, C:E.252 TYD.18: 15 residues within 4Å: Chain D: M.43, F.111, Y.112, G.113, P.114, G.115, L.116, G.117, T.118, S.119, V.247, S.248, E.252, V.253, R.256 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.113, D:G.113, D:G.115, D:G.117, D:T.118, D:T.118, D:T.118, D:S.119, D:S.248 Water bridges: D:I.249, D:I.249

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: R.122, F.123, S.125, I.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125 Water bridges: A:S.125, A:S.127 EDO.14: 4 residues within 4Å: Chain C: R.122, F.123, S.125, I.126 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.125 Water bridges: C:S.125, C:S.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, H.A. et al., The structure of glucose-1-phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA-type enzymes. Protein Sci. (2018)

Release Date

2018-02-21

Peptides

Glucose-1-phosphate thymidylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glucose-1-phosphate thymidylyltransferase

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