SMTL ID : 4iz9.1

Crystal structure of an acetate kinase from Mycobacterium avium bound to an unknown acid-ApCpp conjugate and manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: E.378 Ligands: APC.2, SIN.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.378, H2O.6, H2O.6, H2O.6 MN.8: 3 residues within 4Å: Chain B: E.378 Ligands: APC.9, SIN.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.378, H2O.17, H2O.17, H2O.17

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.2: 16 residues within 4Å: Chain A: N.19, K.26, R.85, G.204, N.205, R.275, D.276, F.277, R.278, A.323, G.324, I.325, N.328, D.329 Ligands: MN.1, SIN.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.19, A:K.26, A:R.85, A:N.205, A:R.275, A:D.276, A:F.277, A:R.278, A:R.278, A:G.324, A:N.328 Water bridges: A:R.278, A:N.328, A:N.328, A:N.328 Salt bridges: A:K.26 pi-Cation interactions: A:R.278 APC.9: 16 residues within 4Å: Chain B: N.19, K.26, R.85, G.204, N.205, R.275, D.276, F.277, R.278, A.323, G.324, I.325, N.328, D.329 Ligands: MN.8, SIN.10 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.19, B:K.26, B:R.85, B:N.205, B:R.275, B:D.276, B:F.277, B:R.278, B:R.278, B:G.324, B:N.328 Water bridges: B:R.278, B:N.328, B:N.328, B:N.328 Salt bridges: B:K.26 pi-Cation interactions: B:R.278

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.3: 8 residues within 4Å: Chain A: H.174, H.202, G.204, N.205, G.206 Ligands: MN.1, APC.2, EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.205 Hydrogen bonds: A:N.205 Water bridges: A:R.85, A:G.324 Salt bridges: A:R.85, A:H.174, A:H.202 SIN.10: 8 residues within 4Å: Chain B: H.174, H.202, G.204, N.205, G.206 Ligands: MN.8, APC.9, EDO.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.205 Hydrogen bonds: B:N.205 Water bridges: B:R.85, B:G.324 Salt bridges: B:R.85, B:H.174, B:H.202

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

EDO.4: 9 residues within 4Å: Chain A: R.85, V.87, D.142, H.174, G.206, M.222, P.226, R.235 Ligands: SIN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.142, A:D.142, A:R.235, A:R.235 EDO.5: 4 residues within 4Å: Chain A: P.151, A.154, T.155, R.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.155 Water bridges: A:T.155, A:D.164, A:R.169 EDO.6: 5 residues within 4Å: Chain A: Q.292, Y.295, S.296, T.299, D.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.292, A:D.335 Water bridges: A:Q.292 EDO.7: 6 residues within 4Å: Chain A: L.310, G.314, H.315, T.316 Chain B: E.342, L.343 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.310, A:H.315, A:T.316, A:T.316, B:E.342, B:E.342 EDO.11: 9 residues within 4Å: Chain B: R.85, V.87, D.142, H.174, G.206, M.222, P.226, R.235 Ligands: SIN.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.142, B:R.235, B:R.235 EDO.12: 4 residues within 4Å: Chain B: P.151, A.154, T.155, R.169 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.155 Water bridges: B:R.169 EDO.13: 5 residues within 4Å: Chain B: Q.292, Y.295, S.296, T.299, D.335 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.292, B:D.335 Water bridges: B:Q.292 EDO.14: 6 residues within 4Å: Chain A: E.342, L.343 Chain B: L.310, G.314, H.315, T.316 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.342, B:L.310, B:T.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2015)

Release Date

2013-02-20

Peptides

Acetate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Acetate kinase

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