SMTL ID : 4xt8.1

Crystal structure of Rv2671 from Mycobacterium tuberculosis in complex with NADP+ and trimetrexate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 29 residues within 4Å: Chain A: F.45, I.46, A.53, T.54, G.57, T.58, S.59, G.84, V.85, G.86, T.87, I.90, E.91, V.120, T.121, R.122, S.123, V.173, E.175, E.193, G.194, G.195, P.196, T.197, L.198, T.201, R.225 Ligands: TMQ.2, PEG.5 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.45, A:F.45, A:T.87 Hydrogen bonds: A:I.46, A:I.46, A:S.59, A:S.59, A:G.84, A:G.84, A:V.85, A:G.86, A:T.87, A:T.87, A:T.121, A:T.121, A:R.122, A:S.123, A:E.175, A:G.195, A:T.197, A:L.198, A:T.201, A:R.225 Water bridges: A:R.89, A:R.89, A:R.89, A:S.123 NAP.8: 29 residues within 4Å: Chain B: F.45, I.46, A.53, T.54, G.57, T.58, S.59, G.84, V.85, G.86, T.87, I.90, E.91, V.120, T.121, R.122, S.123, V.173, E.175, E.193, G.194, G.195, P.196, T.197, L.198, T.201, R.225 Ligands: TMQ.9, PEG.12 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:F.45, B:F.45, B:T.87 Hydrogen bonds: B:I.46, B:I.46, B:S.59, B:S.59, B:G.84, B:G.84, B:V.85, B:G.86, B:T.87, B:E.91, B:T.121, B:R.122, B:S.123, B:G.195, B:T.197, B:T.197, B:L.198, B:T.201, B:T.201, B:R.225 Water bridges: B:R.89, B:R.89, B:R.89, B:S.123, B:T.229

2 x TMQ: TRIMETREXATE(Non-covalent)

TMQ.2: 14 residues within 4Å: Chain A: N.44, F.45, I.46, S.59, G.60, A.63, D.67, F.71, R.75, E.91, Y.93, E.193, T.214 Ligands: NAP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.63, A:F.71, A:Y.93 Hydrogen bonds: A:N.44, A:N.44, A:N.44, A:R.75, A:E.91, A:T.214 Water bridges: A:R.75 Salt bridges: A:D.67 pi-Stacking: A:F.71, A:F.71 TMQ.9: 14 residues within 4Å: Chain B: N.44, F.45, I.46, S.59, G.60, A.63, D.67, F.71, R.75, E.91, Y.93, E.193, T.214 Ligands: NAP.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.63, B:F.71, B:Y.93 Hydrogen bonds: B:N.44, B:N.44, B:N.44, B:R.75, B:E.91, B:T.214 Water bridges: B:R.75 Salt bridges: B:D.67 pi-Stacking: B:F.71, B:F.71

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

PEG.3: 8 residues within 4Å: Chain A: C.240, A.241, H.242, V.243 Chain B: L.16, L.17, T.245, G.249 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.245, B:T.245, A:V.243 PEG.5: 3 residues within 4Å: Chain A: R.122, T.197 Ligands: NAP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122 PEG.10: 8 residues within 4Å: Chain A: L.16, L.17, T.245, G.249 Chain B: C.240, A.241, H.242, V.243 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.245, B:V.243 PEG.12: 3 residues within 4Å: Chain B: R.122, T.197 Ligands: NAP.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.122

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: A.61, M.62, A.63, G.64, P.65, Y.218, Y.250 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.62, A:Y.218, A:Y.218, A:Y.250 GOL.11: 8 residues within 4Å: Chain B: A.61, M.62, A.63, G.64, P.65, Y.218, Y.250 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.62, B:Y.218, B:Y.250

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

EDO.6: 7 residues within 4Å: Chain A: G.64, P.65, G.66, D.246, S.248, Y.250 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.66, A:D.246, A:S.248 Water bridges: A:D.67, A:S.248 EDO.7: 5 residues within 4Å: Chain A: D.79, R.106, Q.111, S.112, L.187 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.79, A:R.106, A:Q.111, A:S.112, A:S.112, A:Q.116 EDO.13: 7 residues within 4Å: Chain B: G.64, P.65, G.66, D.246, S.248, Y.250 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.66, B:D.246, B:S.248 Water bridges: B:D.67, B:S.248 EDO.14: 5 residues within 4Å: Chain B: D.79, R.106, Q.111, S.112, L.187 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.106, B:Q.111, B:S.112, B:S.112, B:Q.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, Y.S. et al., Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance. Biochemistry (2016)

Release Date

2016-02-24

Peptides

Rv2671: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Rv2671

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