SMTL ID : 1n5i.1

CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT PH 4.6 (RESOLUTION 1.85 A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: V.8, G.10, A.11, G.12, K.13, R.14, R.153 Ligands: FLC.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13, A:R.14 Water bridges: A:D.9, A:K.13, A:T.15 Salt bridges: A:K.13, A:R.153 SO4.2: 5 residues within 4Å: Chain A: A.154, Q.155, A.161, R.162, R.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.162 Salt bridges: A:R.162, A:R.167 SO4.6: 8 residues within 4Å: Chain B: V.8, G.10, A.11, G.12, K.13, R.14, R.153 Ligands: FLC.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13, B:R.14 Water bridges: B:D.9, B:K.13, B:T.15 Salt bridges: B:K.13, B:R.153 SO4.7: 5 residues within 4Å: Chain B: A.154, Q.155, A.161, R.162, R.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.162 Salt bridges: B:R.162, B:R.167

2 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 10 residues within 4Å: Chain A: V.8, D.9, G.10, A.11, G.12, K.13, R.14, D.94, R.153 Ligands: SO4.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.14 Hydrogen bonds: A:G.10, A:A.11, A:G.12, A:K.13 Water bridges: A:K.13, A:K.13, A:R.14 Salt bridges: A:K.13, A:K.13, A:R.153 FLC.8: 10 residues within 4Å: Chain B: V.8, D.9, G.10, A.11, G.12, K.13, R.14, D.94, R.153 Ligands: SO4.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.14 Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:K.13 Water bridges: B:K.13, B:K.13, B:R.14 Salt bridges: B:K.13, B:K.13, B:R.153

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.4: 12 residues within 4Å: Chain A: D.9, P.37, Y.39, L.52, F.70, R.74, R.95, S.99, N.100, Y.103, D.163, Y.165 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.37, A:Y.103 Hydrogen bonds: A:R.74, A:R.74, A:N.100, A:D.163 Water bridges: A:R.95, A:R.95 Salt bridges: A:R.95 pi-Stacking: A:F.70 TMP.9: 12 residues within 4Å: Chain B: D.9, P.37, Y.39, L.52, F.70, R.74, R.95, S.99, N.100, Y.103, D.163, Y.165 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.37, B:Y.103 Hydrogen bonds: B:Y.39, B:R.74, B:R.74, B:N.100, B:D.163 Water bridges: B:R.95, B:R.95 Salt bridges: B:R.95 pi-Stacking: B:F.70

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 4 residues within 4Å: Chain A: T.33, L.34, Q.41, L.84 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.41, A:T.80 Water bridges: A:A.35, A:A.35, A:A.35, A:R.38, A:H.79, A:T.80, A:T.80 ATP.10: 4 residues within 4Å: Chain B: T.33, L.34, Q.41, L.84 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.41, B:T.80 Water bridges: B:A.35, B:A.35, B:A.35, B:R.38, B:Q.41, B:H.79, B:T.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fioravanti, E. et al., Mycobacterium tuberculosis Thymidylate Kinase: Structural Studies of Intermediates along the Reaction Pathway. J.Mol.Biol. (2003)

Release Date

2003-04-08

Peptides

THYMIDYLATE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

THYMIDYLATE KINASE

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