SMTL ID : 6rjc.1

E.coli transketolase apoenzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.155, N.185, I.187 Ligands: EDO.13, EDO.14 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.187, H2O.9 CA.29: 3 residues within 4Å: Chain B: D.155, N.185, I.187 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.35, H2O.53

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

EDO.2: 8 residues within 4Å: Chain A: I.615, D.617, T.633 Chain B: R.483, V.484, T.485, P.486, K.621 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: A.55, W.307, F.311, F.325, T.326, M.329 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: K.131, T.172, L.173, K.174, I.396, N.397 Ligand excluded by PLIP EDO.5: 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.6: 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.7: 5 residues within 4Å: Chain A: S.559, E.560, L.563, F.645, F.650 Ligand excluded by PLIP EDO.8: 9 residues within 4Å: Chain A: V.409, E.411, F.437, Y.440, H.473 Chain B: G.114, P.115, L.116, E.160 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: Q.525, Q.526, E.527, L.543, K.544, V.565 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain A: G.114, P.115, L.116, E.160 Chain B: V.409, E.411, F.437, Y.440, H.473 Ligand excluded by PLIP EDO.11: 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.12: 10 residues within 4Å: Chain A: W.41, R.42, L.45, K.46, H.47, P.49, A.296, A.299, G.300, K.303 Ligand excluded by PLIP EDO.13: 13 residues within 4Å: Chain A: N.64, H.66, L.116, G.154, D.155, G.156, C.157, I.187, S.188, H.261 Chain B: V.409 Ligands: CA.1, EDO.14 Ligand excluded by PLIP EDO.14: 10 residues within 4Å: Chain A: A.29, N.64, H.66, N.185, I.187, S.188, I.247, H.261 Ligands: CA.1, EDO.13 Ligand excluded by PLIP EDO.15: 10 residues within 4Å: Chain A: H.26, H.100, I.189, H.261 Chain B: L.382, S.385, F.434, D.469, H.473 Ligands: EDO.40 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: D.155, Y.182, D.184, V.193, F.197, T.198, D.199, T.201, M.242 Ligand excluded by PLIP EDO.17: 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.18: 7 residues within 4Å: Chain A: F.434, H.461, L.466, D.469, H.473, R.520 Ligands: EDO.49 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: P.352, A.353, K.354, L.523, A.524, Q.525 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: R.4, L.7, E.38, R.42 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: L.389, S.393, K.394, A.395, E.398, Y.404, H.406 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: E.6, G.278, W.279, K.280, Y.281, I.290 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: A.22, K.23, S.24 Chain B: E.468, P.640 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: A.292, Q.293 Ligand excluded by PLIP EDO.30: 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.31: 4 residues within 4Å: Chain B: Y.505, E.508, R.509 Ligands: EDO.41 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: R.274, E.275, G.278, W.279, K.280 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: S.559, E.560, L.563, F.645, F.650 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain B: A.271, L.272, E.275 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: K.21, A.22, K.88, N.89, F.90, Q.92 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain B: E.6, N.9, G.278, W.279, K.280, Y.281, I.290 Ligand excluded by PLIP EDO.37: 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.38: 6 residues within 4Å: Chain B: K.131, T.172, L.173, K.174, I.396, N.397 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: A.55, W.307, F.311, F.325, T.326, M.329 Ligands: EDO.46 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain B: F.434, H.461, L.466, D.469, H.473, R.520 Ligands: EDO.15 Ligand excluded by PLIP EDO.41: 1 residues within 4Å: Ligands: EDO.31 Ligand excluded by PLIP EDO.42: 10 residues within 4Å: Chain B: W.41, R.42, L.45, K.46, H.47, P.49, A.296, A.299, G.300, K.303 Ligand excluded by PLIP EDO.43: 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.44: 7 residues within 4Å: Chain B: L.389, S.393, K.394, A.395, E.398, Y.404, H.406 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain B: I.246, G.248, F.249, G.250, S.251, A.255, Q.276 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain B: S.53, A.55, T.326, M.329, K.330 Ligands: EDO.39 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain B: A.135, D.399, A.400, A.401 Ligand excluded by PLIP EDO.48: 8 residues within 4Å: Chain B: P.52, S.53, R.57, V.103, G.104, G.108, V.109, E.110 Ligand excluded by PLIP EDO.49: 12 residues within 4Å: Chain A: L.466, E.468, D.469, R.520 Chain B: S.24, G.25, H.26, R.91, G.262, A.263, P.264 Ligands: EDO.18 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain A: T.198 Chain B: G.171, T.172, K.174, Y.208, G.209 Ligand excluded by PLIP

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

NA.25: 7 residues within 4Å: Chain A: Y.148, G.176, I.179, A.231, R.232, V.234, T.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.176 NA.51: 8 residues within 4Å: Chain B: Y.148, G.176, I.179, A.231, R.232, V.234, T.235, K.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.234

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 10 residues within 4Å: Chain A: P.52, S.53, R.57, V.103, G.104, T.106, A.107, G.108, V.109, E.110 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:P.52, A:S.53, A:R.57, A:G.108 Water bridges: A:R.57, A:V.109, A:E.110 GOL.27: 6 residues within 4Å: Chain A: Q.136, F.137, R.139, E.321, E.324, R.328 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.136, A:R.139 Water bridges: A:R.139 GOL.28: 7 residues within 4Å: Chain A: K.342, I.345, A.346, V.501, L.533, A.534, A.537 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.342 Water bridges: A:A.534, A:A.534

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, S. et al., Low-barrier hydrogen bonds in enzyme cooperativity. Nature (2019)

Release Date

2019-09-11

Peptides

Transketolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase 1

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