SMTL ID : 3lv8.1

1.8 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with TMP, thymidine-5'-diphosphate and ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: L.35, E.36, G.37, A.38, G.39, K.40, S.41, T.42, R.171, A.211, Q.213, S.214, I.215, V.218 Ligands: TYD.3, CA.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.37, A:A.38, A:G.39, A:K.40, A:S.41, A:S.41, A:T.42, A:R.171, A:R.171, A:Q.213, A:I.215 Water bridges: A:K.40, A:K.40, A:D.121 Salt bridges: A:K.40 pi-Cation interactions: A:R.171 ADP.11: 16 residues within 4Å: Chain B: L.35, E.36, G.37, A.38, G.39, K.40, S.41, T.42, R.171, A.211, Q.213, S.214, I.215, V.218 Ligands: TYD.13, CA.15 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.37, B:A.38, B:G.39, B:K.40, B:S.41, B:S.41, B:T.42, B:R.171, B:R.171, B:Q.213, B:I.215 Water bridges: B:K.40, B:K.40, B:D.121 Salt bridges: B:K.40 pi-Cation interactions: B:R.171

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

TMP.2: 15 residues within 4Å: Chain A: E.36, E.64, P.65, R.75, K.79, V.96, R.100, R.122, S.126, S.127, Y.130, Q.131, I.181 Ligands: TYD.3, CA.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.64, A:R.122, A:Y.130 Hydrogen bonds: A:R.100, A:Q.131, A:Q.131 Water bridges: A:K.40, A:R.75, A:R.75, A:K.79, A:K.79, A:R.122 Salt bridges: A:R.75, A:K.79, A:R.122 TMP.12: 15 residues within 4Å: Chain B: E.36, E.64, P.65, R.75, K.79, V.96, R.100, R.122, S.126, S.127, Y.130, Q.131, I.181 Ligands: TYD.13, CA.16 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:E.64, B:R.122, B:Y.130 Hydrogen bonds: B:R.100, B:Q.131, B:Q.131 Water bridges: B:K.40, B:R.75, B:R.75, B:K.79, B:K.79, B:R.122, B:E.182 Salt bridges: B:R.75, B:K.79, B:R.122

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

TYD.3: 18 residues within 4Å: Chain A: E.36, E.64, P.65, R.75, K.79, V.96, R.100, R.122, S.126, S.127, Y.130, Q.131, I.181, E.182 Ligands: ADP.1, TMP.2, CA.5, CA.6 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:E.64, A:Y.130 Hydrogen bonds: A:R.75, A:R.100, A:Q.131, A:Q.131 Water bridges: A:G.37, A:K.40, A:R.75, A:R.75, A:K.79, A:K.79, A:K.79, A:K.79, A:R.122 Salt bridges: A:R.75, A:K.79, A:K.79, A:R.122 TYD.13: 18 residues within 4Å: Chain B: E.36, E.64, P.65, R.75, K.79, V.96, R.100, R.122, S.126, S.127, Y.130, Q.131, I.181, E.182 Ligands: ADP.11, TMP.12, CA.15, CA.16 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:E.64, B:Y.130 Hydrogen bonds: B:R.75, B:R.100, B:Q.131, B:Q.131 Water bridges: B:G.37, B:K.40, B:R.75, B:R.75, B:K.79, B:K.79, B:K.79, B:K.79, B:R.122, B:E.182, B:E.182 Salt bridges: B:R.75, B:K.79, B:K.79, B:R.122

12 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 1 residues within 4Å: Chain A: E.116 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.116, A:E.116, H2O.10, H2O.10, H2O.10 CA.5: 2 residues within 4Å: Ligands: ADP.1, TYD.3 No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain A: E.36, E.182 Ligands: TMP.2, TYD.3 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.36, A:E.182, TMP.2, H2O.5, H2O.9 CA.7: 4 residues within 4Å: Chain A: A.200, D.203, D.204, V.206 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.200, A:D.203, H2O.1, H2O.1, H2O.7 CA.8: 1 residues within 4Å: Chain A: N.201 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:N.201, H2O.2, H2O.2, H2O.3, H2O.3 CA.9: 1 residues within 4Å: Chain A: K.154 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain B: E.116 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.116, B:E.116, H2O.21, H2O.21, H2O.21 CA.15: 2 residues within 4Å: Ligands: ADP.11, TYD.13 No protein-ligand interaction detected (PLIP) CA.16: 4 residues within 4Å: Chain B: E.36, E.182 Ligands: TMP.12, TYD.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.36, B:E.182, H2O.16, H2O.20 CA.17: 4 residues within 4Å: Chain B: A.200, D.203, D.204, V.206 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.200, B:D.203, H2O.12, H2O.12, H2O.18 CA.18: 1 residues within 4Å: Chain B: N.201 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:N.201, H2O.13, H2O.13, H2O.14, H2O.14 CA.19: 1 residues within 4Å: Chain B: K.154 No protein-ligand interaction detected (PLIP)

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

CL.10: 3 residues within 4Å: Chain A: G.134, R.135, M.184 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: G.134, R.135, M.184 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halavaty, A.S. et al., 1.8 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with TMP, thymidine-5'-diphosphate and ADP. To be Published

Release Date

2010-03-02

Peptides

Thymidylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate kinase

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