SMTL ID : 6tj9.1

Escherichia coli transketolase in complex with cofactor analog 2'-methoxythiamine and substrate xylulose 5-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.95 Å

Oligo State

homo-dimer

Ligands

2 x 5SP: 5-O-phosphono-D-xylulose(Non-covalent)

5SP.1: 13 residues within 4Å: Chain A: R.358, S.385, F.434, H.461, D.469, H.473, R.520 Chain B: H.26, I.189, H.261, G.262 Ligands: EDO.8, NDQ.18 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.385, A:H.473, B:H.26, B:H.261 Water bridges: A:R.358, A:R.358, A:R.358, A:R.358, B:R.91 Salt bridges: A:R.358, A:H.461, A:R.520 5SP.20: 12 residues within 4Å: Chain A: H.26, I.189, H.261, G.262 Chain B: R.358, S.385, F.434, H.461, D.469, H.473, R.520 Ligands: NDQ.2 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.385, B:H.473, A:H.26, A:H.261 Water bridges: B:R.358, B:R.358, B:R.358, B:R.358 Salt bridges: B:R.358, B:H.461, B:R.520

2 x NDQ: 2-[3-[(4-azanyl-2-methoxy-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate(Non-covalent)

NDQ.2: 26 residues within 4Å: Chain A: A.29, N.64, H.66, G.114, P.115, L.116, G.154, D.155, G.156, E.160, N.185, I.187, S.188, I.189, I.247, H.261 Chain B: D.381, L.382, V.409, E.411, F.434, F.437, Y.440, H.473 Ligands: CA.3, 5SP.20 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.116, A:I.189, B:D.381 Hydrogen bonds: A:G.114, A:L.116, A:D.155, A:G.156, A:E.160, A:N.185 Water bridges: A:A.29, A:N.64, A:D.183, A:D.183, A:D.183, B:T.433 Salt bridges: A:H.66, A:H.66, A:H.261 pi-Stacking: B:F.437 NDQ.18: 26 residues within 4Å: Chain A: D.381, L.382, V.409, E.411, F.434, F.437, Y.440, H.473 Chain B: A.29, N.64, H.66, G.114, P.115, L.116, G.154, D.155, G.156, E.160, N.185, I.187, S.188, I.189, I.247, H.261 Ligands: 5SP.1, CA.19 18 PLIP interactions: 2 interactions with chain A, 16 interactions with chain B Water bridges: A:T.433, B:A.29, B:N.64, B:D.183, B:D.183, B:D.183 pi-Stacking: A:F.437 Hydrophobic interactions: B:L.116, B:I.189 Hydrogen bonds: B:G.114, B:L.116, B:D.155, B:G.156, B:E.160, B:N.185 Salt bridges: B:H.66, B:H.66, B:H.261

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.155, N.185, I.187 Ligands: NDQ.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.187, H2O.5 CA.19: 4 residues within 4Å: Chain B: D.155, N.185, I.187 Ligands: NDQ.18 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.35

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

EDO.4: 11 residues within 4Å: Chain A: F.375, L.376, G.377, T.388, L.389, W.390, S.393, K.394, N.403, Y.404, Y.430 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: W.41, L.45, K.46, H.47, P.49, A.296, A.299, G.300, K.303 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: S.559, E.560, L.563, F.645, F.650 Ligand excluded by PLIP EDO.7: 12 residues within 4Å: Chain A: L.435, D.462, S.463, P.475, V.476, V.479, R.483, R.492, I.517, E.612, A.613, G.614 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: P.384, S.385 Chain B: I.189, H.258, H.261, G.262 Ligands: 5SP.1 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: D.155, Y.182, D.184, G.186, V.193, F.197, T.198, D.199, T.201 Ligand excluded by PLIP EDO.10: 11 residues within 4Å: Chain A: W.41, L.45, K.46, H.47, R.57, D.58, R.59, F.60, Y.80, G.108, E.110 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Y.505, A.537, R.538, A.588, Q.592 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: A.55, W.307, F.311, F.325, T.326, M.329 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: R.4, L.7, R.42, D.43 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: Y.620, V.623, G.624, L.625, N.626, G.627, A.628, I.629 Ligand excluded by PLIP EDO.15: 9 residues within 4Å: Chain A: I.615, D.617, T.633 Chain B: R.483, V.484, T.485, P.486, D.590, K.621 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: Q.136, F.137, R.139, E.321, E.324, R.328 Ligand excluded by PLIP EDO.21: 11 residues within 4Å: Chain B: F.375, L.376, G.377, T.388, L.389, W.390, S.393, K.394, N.403, Y.404, Y.430 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: A.271, E.275 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: R.538, Q.592, D.593 Ligands: EDO.33 Ligand excluded by PLIP EDO.24: 12 residues within 4Å: Chain B: L.435, D.462, S.463, P.475, V.476, V.479, R.483, R.492, I.517, E.612, A.613, G.614 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: K.21, A.22, K.88, N.89, F.90, Q.92 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: Y.505, R.509, D.511, K.591 Ligands: EDO.33 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: S.559, E.560, L.563, F.645, F.650 Ligand excluded by PLIP EDO.28: 11 residues within 4Å: Chain B: W.41, L.45, K.46, H.47, R.57, D.58, R.59, F.60, Y.80, G.108, E.110 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: E.6, G.278, W.279, K.280, Y.281, I.290 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: K.131, T.172, L.173, K.174, I.396, N.397 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain B: Q.549, A.604 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: A.55, W.307, F.311, F.325, T.326, M.329 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Ligands: EDO.23, EDO.26 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.17: 8 residues within 4Å: Chain A: Y.148, G.176, K.177, I.179, A.231, R.232, V.234, T.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.232 NA.34: 7 residues within 4Å: Chain B: Y.148, G.176, I.179, A.231, R.232, V.234, T.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.232, B:V.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rabe von Pappenheim, F. et al., Structural basis for antibiotic action of the B 1 antivitamin 2'-methoxy-thiamine. Nat.Chem.Biol. (2020)

Release Date

2020-07-08

Peptides

Transketolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase 1

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