SMTL ID : 8b8h.1

Structure of DCS-resistant variant D322N of alanine racemase from M. tuberculosis in complex with DCS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

1 x OJQ: [2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl-(3-oxidanyl-1,2-oxazol-4-yl)azanium(Non-covalent)

OJQ.1: 19 residues within 4Å: Chain A: V.43, K.45, Y.49, W.91, K.136, M.173, H.175, N.215, S.216, R.231, P.232, G.233, I.234, Y.367 Chain B: Y.274, Y.293, C.321, M.322 Ligands: L7N.2 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.91 Hydrogen bonds: A:K.45, A:Y.49, A:W.91, A:H.175, A:S.216, A:S.216, A:S.216, A:R.231, A:R.231, A:G.233, A:I.234, A:Y.367, B:Y.274, B:Y.293, B:M.322 Water bridges: A:N.215, A:N.215, A:S.217, B:N.323 pi-Stacking: A:H.175

2 x L7N: (~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylidene-[(4~{R})-3-oxidanylidene-1,2-oxazolidin-4-yl]azanium(Non-covalent)

L7N.2: 19 residues within 4Å: Chain A: V.43, K.45, Y.49, W.91, K.136, M.173, H.175, N.215, S.216, R.231, P.232, G.233, I.234, Y.367 Chain B: Y.274, Y.293, C.321, M.322 Ligands: OJQ.1 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.43, A:W.91 Hydrogen bonds: A:Y.49, A:W.91, A:H.175, A:S.216, A:S.216, A:S.216, A:R.231, A:R.231, A:G.233, A:I.234, A:Y.367, B:Y.274, B:Y.274, B:Y.293, B:M.322 Water bridges: A:K.45, A:N.215, A:N.215, A:S.217, B:Q.324 pi-Stacking: A:H.175 L7N.6: 19 residues within 4Å: Chain A: Y.274, Y.293, C.321, M.322 Chain B: V.43, K.45, Y.49, W.91, K.136, M.173, H.175, N.215, S.216, R.231, P.232, G.233, I.234, Y.367 Ligands: EDO.9 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:Y.274, A:Y.274, A:Y.293, A:M.322, B:Y.49, B:W.91, B:S.216, B:S.216, B:S.216, B:R.231, B:R.231, B:G.233, B:I.234, B:Y.367, B:Y.367 Water bridges: A:Y.274, B:K.45, B:N.215 Hydrophobic interactions: B:V.43, B:W.91 pi-Stacking: B:H.175

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: A.337, D.340 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.340, H2O.5

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

CL.4: 7 residues within 4Å: Chain A: N.323, Q.324, R.376 Chain B: K.45, A.71, L.92 Ligands: EDO.9 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: K.45, A.71, L.92 Chain B: N.323, Q.324, R.376 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: L.308, I.309, N.310, G.311, E.341, A.342, I.343, R.350 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.310, A:N.310, A:G.311, A:E.341 Water bridges: A:E.341, A:E.341

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

EDO.8: 11 residues within 4Å: Chain A: A.294, R.374 Chain B: A.46, D.47, Y.49, G.50, V.370, T.371, P.373, R.374, R.379 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.46, B:R.379 Water bridges: B:G.50, B:T.371, A:R.374 EDO.9: 9 residues within 4Å: Chain A: Q.324 Chain B: K.45, A.71, W.91, L.92, K.136, N.144 Ligands: CL.4, L7N.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.45, B:W.91, B:W.91, B:K.136, B:N.144 EDO.10: 12 residues within 4Å: Chain B: K.136, V.137, D.138, T.139, G.140, L.141, N.142, R.143, N.144, G.145, S.174, H.175 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.136, B:D.138, B:R.143, B:H.175 Water bridges: B:T.139, B:T.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Chiara, C. et al., Structure of the d-Cycloserine-Resistant Variant D322N of Alanine Racemase from Mycobacterium tuberculosis . Acs Bio Med Chem Au (2023)

Release Date

2023-04-05

Peptides

Alanine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine racemase

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