SMTL ID : 2pan.1 (1 other biounit)

Crystal structure of E. coli glyoxylate carboligase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.469, N.496, Y.498 Ligands: TPP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.469, A:Y.498 MG.2: 7 residues within 4Å: Chain A: F.474, L.475, E.477 Chain C: F.474, L.475, E.477 Ligands: MG.13 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:F.474, A:E.477, C:F.474, C:E.477 MG.7: 4 residues within 4Å: Chain B: D.469, N.496, Y.498 Ligands: TPP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.469, B:Y.498 MG.8: 7 residues within 4Å: Chain B: F.474, L.475, E.477 Chain D: F.474, L.475, E.477 Ligands: MG.19 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Metal complexes: B:F.474, B:E.477, D:F.474, D:E.477 MG.12: 4 residues within 4Å: Chain C: D.469, N.496, Y.498 Ligands: TPP.15 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.469, C:Y.498 MG.13: 7 residues within 4Å: Chain A: F.474, L.475, E.477 Chain C: F.474, L.475, E.477 Ligands: MG.2 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Metal complexes: A:F.474, A:E.477, C:F.474, C:E.477 MG.18: 4 residues within 4Å: Chain D: D.469, N.496, Y.498 Ligands: TPP.21 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.469, D:Y.498 MG.19: 7 residues within 4Å: Chain B: F.474, L.475, E.477 Chain D: F.474, L.475, E.477 Ligands: MG.8 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:F.474, D:E.477, B:F.474, B:E.477

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.3: 35 residues within 4Å: Chain A: S.117, R.177, P.178, G.234, G.235, G.236, N.239, A.240, T.260, L.261, M.262, V.278, G.279, L.280, Q.281, T.282, G.301, N.302, R.303, A.305, R.307, H.308, D.325, I.326, E.327, Q.330, S.343, D.344, A.345, I.416, Q.420, I.421, G.439, Q.440 Chain C: F.137 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.261, A:Q.281, A:T.282, A:I.416, A:I.421, C:F.137 Hydrogen bonds: A:R.177, A:G.235, A:T.260, A:T.260, A:L.261, A:V.278, A:L.280, A:Q.281, A:T.282, A:R.303, A:I.326, A:Q.330, A:D.344, A:A.345, A:G.439 Water bridges: A:A.115, A:D.116, A:D.116, A:R.303, A:A.305 Salt bridges: A:R.303, A:R.303 FAD.9: 35 residues within 4Å: Chain B: S.117, R.177, P.178, G.234, G.235, G.236, N.239, A.240, T.260, L.261, M.262, V.278, G.279, L.280, Q.281, T.282, G.301, N.302, R.303, A.305, R.307, H.308, D.325, I.326, E.327, Q.330, S.343, D.344, A.345, I.416, Q.420, I.421, G.439, Q.440 Chain D: F.137 26 PLIP interactions: 1 interactions with chain D, 25 interactions with chain B Hydrophobic interactions: D:F.137, B:L.261, B:Q.281, B:T.282, B:I.416, B:I.421 Hydrogen bonds: B:R.177, B:G.235, B:T.260, B:L.261, B:V.278, B:L.280, B:Q.281, B:T.282, B:T.282, B:R.303, B:R.303, B:H.308, B:I.326, B:Q.330, B:D.344, B:D.344, B:A.345, B:G.439 Salt bridges: B:R.303, B:R.303 FAD.14: 35 residues within 4Å: Chain A: F.137 Chain C: S.117, R.177, P.178, G.234, G.235, G.236, N.239, A.240, T.260, L.261, M.262, V.278, G.279, L.280, Q.281, T.282, G.301, N.302, R.303, A.305, R.307, H.308, D.325, I.326, E.327, Q.330, S.343, D.344, A.345, I.416, Q.420, I.421, G.439, Q.440 30 PLIP interactions: 29 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.261, C:Q.281, C:T.282, C:I.416, C:I.421, A:F.137 Hydrogen bonds: C:R.177, C:G.235, C:T.260, C:L.261, C:V.278, C:L.280, C:Q.281, C:T.282, C:T.282, C:R.303, C:H.308, C:I.326, C:Q.330, C:D.344, C:D.344, C:A.345, C:G.439 Water bridges: C:A.115, C:D.116, C:R.303, C:R.303, C:A.305 Salt bridges: C:R.303, C:R.303 FAD.20: 35 residues within 4Å: Chain B: F.137 Chain D: S.117, R.177, P.178, G.234, G.235, G.236, N.239, A.240, T.260, L.261, M.262, V.278, G.279, L.280, Q.281, T.282, G.301, N.302, R.303, A.305, R.307, H.308, D.325, I.326, E.327, Q.330, S.343, D.344, A.345, I.416, Q.420, I.421, G.439, Q.440 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.261, D:Q.281, D:T.282, D:I.416, D:I.421, B:F.137 Hydrogen bonds: D:R.177, D:G.235, D:T.260, D:T.260, D:L.261, D:V.278, D:L.280, D:Q.281, D:T.282, D:R.303, D:R.303, D:I.326, D:Q.330, D:D.344, D:A.345, D:G.439 Water bridges: D:D.116 Salt bridges: D:R.303, D:R.303

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 26 residues within 4Å: Chain A: I.416, G.417, L.418, S.419, G.442, L.444, G.468, D.469, F.470, D.471, F.474, N.496, Y.498, L.499, G.500, L.501, I.502 Chain C: V.48, P.49, V.74, T.98, P.101, A.102, D.105, Q.138 Ligands: MG.1 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.470, A:F.474, A:L.499, A:L.499, A:I.502, C:V.74, C:T.98 Hydrogen bonds: A:L.418, A:S.419, A:G.442, A:L.444, A:G.468, A:D.469, A:F.470, A:D.471, A:N.496, A:G.500, A:L.501, C:Q.138 Water bridges: A:S.419 TPP.10: 26 residues within 4Å: Chain B: I.416, G.417, L.418, S.419, G.442, L.444, G.468, D.469, F.470, D.471, F.474, N.496, Y.498, L.499, G.500, L.501, I.502 Chain D: V.48, P.49, V.74, T.98, P.101, A.102, D.105, Q.138 Ligands: MG.7 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:F.470, B:F.474, B:L.499, B:L.499, B:I.502, D:V.74, D:T.98 Hydrogen bonds: B:L.418, B:S.419, B:G.442, B:L.444, B:D.469, B:F.470, B:D.471, B:G.500, B:L.501, D:Q.138 Water bridges: B:N.496 TPP.15: 26 residues within 4Å: Chain A: V.48, P.49, V.74, T.98, P.101, A.102, D.105, Q.138 Chain C: I.416, G.417, L.418, S.419, G.442, L.444, G.468, D.469, F.470, D.471, F.474, N.496, Y.498, L.499, G.500, L.501, I.502 Ligands: MG.12 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.470, C:F.474, C:L.499, C:L.499, C:I.502, A:V.74, A:T.98 Hydrogen bonds: C:L.418, C:S.419, C:G.442, C:L.444, C:G.468, C:D.469, C:F.470, C:D.471, C:N.496, C:G.500, C:L.501, A:Q.138 Water bridges: C:S.419 TPP.21: 26 residues within 4Å: Chain B: V.48, P.49, V.74, T.98, P.101, A.102, D.105, Q.138 Chain D: I.416, G.417, L.418, S.419, G.442, L.444, G.468, D.469, F.470, D.471, F.474, N.496, Y.498, L.499, G.500, L.501, I.502 Ligands: MG.18 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:F.470, D:F.474, D:L.499, D:L.499, D:I.502, B:V.74, B:T.98 Hydrogen bonds: D:L.418, D:S.419, D:G.442, D:L.444, D:D.469, D:F.470, D:D.471, D:N.496, D:G.500, D:L.501, B:Q.138

4 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.5: 3 residues within 4Å: Chain A: Q.281, M.586, G.587 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.281 DTT.11: 4 residues within 4Å: Chain B: Q.281, M.586, G.587, S.588 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.307, B:S.588, B:S.588 DTT.16: 3 residues within 4Å: Chain C: Q.281, M.586, G.587 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Q.281 DTT.22: 4 residues within 4Å: Chain D: Q.281, M.586, G.587, S.588 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.307, D:S.588, D:S.588

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 5 residues within 4Å: Chain A: V.593, M.594, E.595, F.596, E.597 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.593, A:E.595 1PE.17: 5 residues within 4Å: Chain C: V.593, M.594, E.595, F.596, E.597 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.593, C:E.595

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaplun, A. et al., Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-dependent enzymes. Nat.Chem.Biol. (2008)

Release Date

2008-01-01

Peptides

Glyoxylate carboligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glyoxylate carboligase

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