SMTL ID : 6scz.1

Mycobacterium tuberculosis alanine racemase inhibited by DCS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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 GOL.2: 6 residues within 4Å: Chain A: H.26, D.247, G.249, L.250, V.251 Ligands: PEG.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.26, A:G.249 Water bridges: A:D.247 GOL.3: 4 residues within 4Å: Chain A: P.243, A.244, G.246 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.247 GOL.4: 5 residues within 4Å: Chain A: P.243, A.244, Q.356, D.360 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.356, A:D.360 GOL.28: 7 residues within 4Å: Chain B: A.191, T.195, D.224, L.225, T.226, F.227 Ligands: GOL.29 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.224, B:T.226 Water bridges: B:T.195, B:T.226 GOL.29: 8 residues within 4Å: Chain B: L.198, F.208, E.209, V.210, A.211, F.227, D.228 Ligands: GOL.28 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.208, B:D.228 Water bridges: B:F.208 GOL.30: 8 residues within 4Å: Chain B: L.308, I.309, N.310, G.311, E.341, A.342, I.343, R.350 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.310, B:G.311, B:E.341, B:R.350

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain A: A.337, D.340 Ligands: TRS.27 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.340, H2O.6, H2O.7

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

CL.6: 5 residues within 4Å: Chain A: Q.324 Chain B: W.91, L.92, K.136, N.144 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: S.113, L.114, Q.150 Ligand excluded by PLIP CL.31: 7 residues within 4Å: Chain B: K.136, D.138, L.141, N.142, R.143, N.144, G.145 Ligand excluded by PLIP

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

EDO.8: 3 residues within 4Å: Chain A: H.26, R.29, V.30 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: A.179, I.365, Y.367 Chain B: Y.274, Y.293, R.299, R.319 Ligands: L7N.25, OJQ.26 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: K.264, S.265 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: G.303, R.304, L.305, E.306, P.315 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: A.35, G.36, H.37, A.38, P.223, T.226 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: G.269, E.270, G.271, H.276, I.279 Ligands: EDO.40 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: P.148, A.196, F.197, Q.200 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: D.357, D.360, L.361 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: R.282, R.312, R.313, C.314, P.315, D.328, L.329, G.330 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain A: I.291, G.292, A.294, D.295, M.322, D.323, G.375, R.376 Chain B: A.46, E.75 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: R.313, E.352, P.353, T.354, D.357 Ligand excluded by PLIP EDO.32: 13 residues within 4Å: Chain B: A.179, D.180, S.216, S.217, I.234, S.240, P.241, V.242, P.243, H.366, Y.367 Ligands: EDO.33, OJQ.49 Ligand excluded by PLIP EDO.33: 9 residues within 4Å: Chain A: Y.274, Y.293, R.299, R.319 Chain B: A.179, I.365, Y.367 Ligands: EDO.32, OJQ.49 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain B: H.26, D.247, G.249, L.250, V.251 Ligands: EDO.36, PEG.44 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: D.118, L.121, H.122 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: V.251, I.349 Ligands: EDO.34, EDO.41 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: E.25, H.26, R.29 Ligands: EDO.41 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain B: A.199, R.202, E.203 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain B: Q.192, T.195, A.196, A.199 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain A: H.276 Chain B: V.177, Y.178, D.184, I.186 Ligands: EDO.13 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain B: D.20, G.22, A.23, H.26, V.251 Ligands: EDO.36, EDO.37 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain A: A.261, L.262, E.338 Chain B: P.95, S.113, R.115, Q.116 Ligand excluded by PLIP

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.19: 6 residues within 4Å: Chain A: D.20, A.23, V.251, P.347, I.349 Ligands: GOL.2 No protein-ligand interaction detected (PLIP) PEG.20: 7 residues within 4Å: Chain A: A.191, Q.192, T.195, D.224, L.225, T.226, F.227 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.191, A:T.195 PEG.21: 13 residues within 4Å: Chain A: F.298, R.299, S.300, V.362, T.364, E.368 Chain B: F.298, R.299, S.300, V.362, G.363, T.364, E.368 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.364, A:R.299, A:S.300 Water bridges: B:S.300, A:E.368 PEG.22: 8 residues within 4Å: Chain A: D.138, T.139, G.140, N.142, P.148, R.193, F.197 Chain B: E.270 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.138, A:N.142, B:E.270 Water bridges: A:R.193, A:R.193 PEG.43: 5 residues within 4Å: Chain A: D.74 Chain B: L.14, G.375, R.376, T.378 No protein-ligand interaction detected (PLIP) PEG.44: 9 residues within 4Å: Chain B: H.26, V.30, E.33, H.34, M.220, M.248, G.249 Ligands: EDO.34, PEG.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.34 PEG.45: 6 residues within 4Å: Chain B: H.34, M.220, A.221, L.245, M.248 Ligands: PEG.44 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.248 Water bridges: B:H.34

5 x P4K: polyethylene glycol(Non-covalent)

P4K.23: 6 residues within 4Å: Chain A: P.182, D.183, M.220, A.221, R.222, P.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.220 P4K.24: 6 residues within 4Å: Chain A: A.259, E.338, G.339 Chain B: P.95, G.96 Ligands: TRS.27 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.115 P4K.46: 6 residues within 4Å: Chain B: P.182, D.183, A.221, R.222, P.223, D.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.221 Water bridges: B:R.222, B:R.222 P4K.47: 10 residues within 4Å: Chain B: E.33, H.34, A.35, G.36, H.37, A.38, P.223, T.226, F.227, D.228 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.37 P4K.48: 8 residues within 4Å: Chain B: Q.39, P.87, Q.108, T.132, R.168, R.170, E.209, V.210 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.67, B:R.168, B:R.170, B:R.170

1 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.25: 22 residues within 4Å: Chain A: V.43, K.45, Y.49, W.91, K.136, R.143, M.173, H.175, A.179, 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: EDO.9, OJQ.26 26 PLIP interactions: 19 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:W.91 Hydrogen bonds: A:K.45, A:Y.49, A:W.91, A:R.143, 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, A:Y.367, B:Y.274, B:Y.274, B:Y.293, B:M.322 Water bridges: A:N.215, A:N.215, A:S.217, B:D.323, B:D.323, B:Q.324 pi-Stacking: A:H.175

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

OJQ.26: 22 residues within 4Å: Chain A: V.43, K.45, Y.49, W.91, K.136, R.143, M.173, H.175, A.179, 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: EDO.9, L7N.25 26 PLIP interactions: 19 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:W.91 Hydrogen bonds: A:K.45, A:Y.49, A:W.91, A:R.143, 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, A:Y.367, B:Y.274, B:Y.274, B:Y.293, B:M.322 Water bridges: A:N.215, A:N.215, A:S.217, B:D.323, B:Q.324, B:Q.324 pi-Stacking: A:H.175 OJQ.49: 22 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, R.143, M.173, H.175, A.179, N.215, S.216, R.231, P.232, G.233, I.234, Y.367 Ligands: EDO.32, EDO.33 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.91 Hydrogen bonds: B:K.45, B:Y.49, B:W.91, B:R.143, B:H.175, 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, A:Y.274, A:Y.293, A:M.322 Water bridges: B:S.217, A:D.323 pi-Stacking: B:H.175

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.27: 5 residues within 4Å: Chain A: E.338, G.339, D.340 Ligands: CA.5, P4K.24 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.338, A:G.339, A:D.340, A:D.340 TRS.50: 9 residues within 4Å: Chain A: E.270 Chain B: D.138, T.139, G.140, N.142, G.147, P.148, R.193, F.197 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.270, B:D.138 Water bridges: B:D.138, B:N.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Chiara, C. et al., D-Cycloserine destruction by alanine racemase and the limit of irreversible inhibition. Nat.Chem.Biol. (2020)

Release Date

2020-04-01

Peptides

Alanine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine racemase