SMTL ID : 6b5e.1 (1 other biounit)

Mycobacterium tuberculosis RmlA in complex with dTDP-glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

5 x DAU: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE(Non-covalent)

DAU.1: 27 residues within 4Å: Chain A: L.6, A.7, G.8, G.9, K.23, Q.24, Q.80, P.83, D.84, G.85, L.86, L.106, G.107, D.108, N.109, Y.142, G.143, E.158, K.159, V.169, G.171, E.193, T.197, W.220, D.222 Ligands: MG.2, CL.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.86 Hydrogen bonds: A:G.8, A:G.9, A:Q.80, A:Q.80, A:G.85, A:G.107, A:D.108, A:D.108, A:N.109, A:N.109, A:G.143, A:E.158, A:V.169, A:T.197 Water bridges: A:R.191, A:R.191, A:R.191, A:R.191, A:D.222, A:D.222 Salt bridges: A:K.23, A:K.159, A:K.159 DAU.6: 26 residues within 4Å: Chain B: L.6, A.7, G.8, G.9, K.23, Q.24, Q.80, P.83, D.84, G.85, L.86, L.106, G.107, D.108, N.109, Y.142, G.143, E.158, K.159, V.169, G.171, E.193, T.197, W.220, D.222 Ligands: MG.7 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.86 Hydrogen bonds: B:G.8, B:G.9, B:Q.80, B:Q.80, B:G.85, B:G.107, B:D.108, B:D.108, B:N.109, B:N.109, B:G.143, B:E.158, B:V.169, B:T.197 Water bridges: B:K.23, B:R.191, B:R.191 Salt bridges: B:K.23, B:K.159, B:K.159 DAU.11: 25 residues within 4Å: Chain C: L.6, A.7, G.8, G.9, K.23, Q.24, Q.80, P.83, D.84, G.85, L.86, L.106, G.107, D.108, N.109, Y.142, G.143, E.158, K.159, V.169, G.171, T.197, W.220, D.222 Ligands: MG.13 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:L.86 Hydrogen bonds: C:G.8, C:G.9, C:Q.80, C:Q.80, C:G.85, C:G.107, C:D.108, C:D.108, C:N.109, C:N.109, C:G.143, C:E.158, C:V.169, C:D.222 Water bridges: C:R.13, C:R.13, C:K.23, C:D.108, C:Y.173, C:Y.173, C:R.191, C:T.197, C:D.222 Salt bridges: C:K.23, C:K.159, C:K.159 DAU.12: 14 residues within 4Å: Chain C: M.43, 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 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.113, C:G.113, C:G.115, C:L.116, C:G.117, C:T.118, C:T.118, C:S.119, C:S.119, C:S.119, C:S.248 Water bridges: C:I.249, C:I.249, C:R.256 DAU.14: 26 residues within 4Å: Chain D: L.6, A.7, G.8, G.9, K.23, Q.24, Q.80, P.83, D.84, G.85, L.86, L.106, G.107, D.108, N.109, Y.142, G.143, E.158, K.159, V.169, G.171, E.193, T.197, W.220, D.222 Ligands: MG.15 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:L.86 Hydrogen bonds: D:G.8, D:G.9, D:Q.80, D:Q.80, D:G.85, D:G.107, D:D.108, D:D.108, D:N.109, D:N.109, D:G.143, D:E.158, D:V.169, D:D.222 Water bridges: D:K.23, D:K.159, D:K.159, D:Y.173, D:Y.173 Salt bridges: D:K.23, D:K.159, D:K.159

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.23, D.108, D.222 Ligands: DAU.1 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.108, A:D.222, H2O.1, H2O.4, DAU.1 MG.7: 4 residues within 4Å: Chain B: K.23, D.108, D.222 Ligands: DAU.6 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.108, B:D.222, DAU.6, H2O.11, H2O.12 MG.8: 1 residues within 4Å: Chain B: R.2 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain C: K.23, D.108, D.222 Ligands: DAU.11 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:D.108, C:D.222, DAU.11, H2O.21, H2O.21 MG.15: 4 residues within 4Å: Chain D: K.23, D.108, D.222 Ligands: DAU.14 5 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: D:D.108, D:D.222, DAU.14, H2O.26, H2O.27

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

TYD.3: 14 residues within 4Å: Chain A: M.43, 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 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.113, A:G.113, A:G.115, A:G.117, A:T.118, A:S.119, A:S.119, A:S.248 Water bridges: A:Y.112, A:Y.112, A:I.249, A:E.252, A:Y.280, A:Y.280 TYD.9: 14 residues within 4Å: Chain B: M.43, 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 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.113, B:G.113, B:G.115, B:G.117, B:T.118, B:S.119, B:S.119, B:S.248 Water bridges: B:Y.112, B:Y.112, B:I.249, B:I.249, B:R.256, C:R.216 TYD.16: 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 13 PLIP interactions: 13 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:S.119, D:S.119, D:S.248 Water bridges: D:I.249, D:I.249, D:Y.280, D:Y.280

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: G.11, K.23 Ligands: DAU.1 Ligand excluded by PLIP

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

EDO.5: 3 residues within 4Å: Chain A: A.58, H.62, T.79 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.62

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 3 residues within 4Å: Chain B: M.1, D.100, S.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.1, B:D.100 Water bridges: B:S.101

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
F

D
H

Glucose-1-phosphate thymidylyltransferase

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