SMTL ID : 1h16.1

Pyruvate Formate-Lyase (E.coli) in complex with Pyruvate and CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

2 x COA: COENZYME A(Non-covalent)

COA.1: 13 residues within 4Å: Chain A: K.116, M.117, N.145, Q.146, F.149, D.150, Y.152, L.157, R.160, K.161 Chain B: F.200, H.227 Ligands: MG.10 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.149, B:F.200 Hydrogen bonds: A:N.145, A:N.145, A:Q.146, A:F.149, A:D.150, A:R.160 Water bridges: A:L.157, A:K.161, A:K.161, A:E.322, A:E.322 Salt bridges: A:K.161, A:K.161 pi-Stacking: A:F.149, A:F.149 COA.16: 13 residues within 4Å: Chain A: F.200, H.227 Chain B: K.116, M.117, N.145, Q.146, F.149, D.150, Y.152, L.157, R.160, K.161 Ligands: MG.25 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:F.200, B:F.149 Hydrogen bonds: B:N.145, B:N.145, B:Q.146, B:F.149, B:D.150, B:R.160 Water bridges: B:L.157, B:K.161, B:K.161, B:E.322, B:E.322, B:E.322 Salt bridges: B:K.161, B:K.161 pi-Stacking: B:F.149, B:F.149

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 10 residues within 4Å: Chain A: R.176, A.272, A.273, F.327, W.333, C.418, F.432, R.435, L.604, I.606 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.272, A:F.327, A:W.333, A:F.432 Water bridges: A:C.419 Salt bridges: A:R.176, A:R.435 PYR.17: 10 residues within 4Å: Chain B: R.176, A.272, A.273, F.327, W.333, C.418, F.432, R.435, L.604, I.606 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.272, B:F.327, B:W.333, B:F.432 Water bridges: B:C.419 Salt bridges: B:R.176, B:R.435

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

NA.3: 4 residues within 4Å: Chain A: A.652, L.654, E.700, G.701 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.656, A:E.700 Water bridges: A:E.700 NA.4: 4 residues within 4Å: Chain A: E.214 Chain B: E.214, Q.215, R.218 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:R.218 Hydrogen bonds: A:Y.499 NA.5: 3 residues within 4Å: Chain A: T.80, I.81, S.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.81 NA.6: 3 residues within 4Å: Chain A: G.687, L.688 Ligands: PG4.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.687 NA.7: 2 residues within 4Å: Chain A: Q.589, P.599 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.589 NA.8: 2 residues within 4Å: Chain A: M.58, K.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.62, A:K.62 NA.9: 1 residues within 4Å: Chain B: F.112 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.269, B:Q.269 NA.18: 4 residues within 4Å: Chain B: A.652, L.654, E.700, G.701 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.652, B:F.656, B:E.700 Water bridges: B:E.700 NA.19: 4 residues within 4Å: Chain A: E.214, Q.215, R.218 Chain B: E.214 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.214, B:Y.499 Water bridges: A:R.218 NA.20: 3 residues within 4Å: Chain B: T.80, I.81, S.268 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.81 NA.21: 3 residues within 4Å: Chain B: G.687, L.688 Ligands: PG4.30 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.687 NA.22: 2 residues within 4Å: Chain B: Q.589, P.599 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.589 NA.23: 2 residues within 4Å: Chain B: M.58, K.62 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.62, B:K.62 Water bridges: B:E.59 NA.24: 1 residues within 4Å: Chain A: F.112 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.268, A:Q.269, A:Q.269

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.10: 1 residues within 4Å: Ligands: COA.1 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Ligands: COA.16 No protein-ligand interaction detected (PLIP)

4 x DTL: L-TREITOL(Non-covalent)

DTL.11: 7 residues within 4Å: Chain A: E.225, R.228, Q.232 Chain B: T.138, E.139, Y.140, K.142 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.140, A:R.228, A:Q.232 Water bridges: B:T.138, B:E.139, B:T.143, A:R.141, A:E.225, A:R.228 DTL.12: 9 residues within 4Å: Chain A: H.68, A.69, P.70, R.107, Y.125, D.324, G.329, D.330, S.741 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.125, A:Y.125, A:D.324 Water bridges: A:R.107, A:R.107, A:R.107, A:R.319, A:G.329, A:G.329, A:D.330 DTL.26: 7 residues within 4Å: Chain A: T.138, E.139, Y.140, K.142 Chain B: E.225, R.228, Q.232 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.228, B:Q.232, A:Y.140 Water bridges: B:R.141, B:E.225, B:E.225, B:R.228, A:T.138, A:E.139, A:T.143 DTL.27: 9 residues within 4Å: Chain B: H.68, A.69, P.70, R.107, Y.125, D.324, G.329, D.330, S.741 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.125, B:D.324 Water bridges: B:R.107, B:R.107, B:R.107, B:R.319, B:G.329, B:G.329, B:D.330, B:D.330

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.13: 4 residues within 4Å: Chain A: E.40, S.41, L.43, Y.361 No protein-ligand interaction detected (PLIP) PG4.14: 5 residues within 4Å: Chain A: A.198, Q.199, S.202, R.516, D.517 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.202, A:R.516, A:D.517 Water bridges: A:D.195, A:D.195, A:D.195, A:D.195, A:D.195, A:R.516 PG4.15: 8 residues within 4Å: Chain A: V.645, L.648, T.649, G.687, L.688, G.691, Y.692 Ligands: NA.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.649 PG4.28: 4 residues within 4Å: Chain B: E.40, S.41, L.43, Y.361 No protein-ligand interaction detected (PLIP) PG4.29: 5 residues within 4Å: Chain B: A.198, Q.199, S.202, R.516, D.517 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.202, B:R.516 Water bridges: B:D.195, B:D.195, B:D.195, B:R.516 PG4.30: 8 residues within 4Å: Chain B: V.645, L.648, T.649, G.687, L.688, G.691, Y.692 Ligands: NA.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Becker, A. et al., X-Ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and Coa.How the Enzyme Uses the Cys-418 Thiyl Radical for Pyruvate Cleavage. J.Biol.Chem. (2002)

Release Date

2002-11-01

Peptides

FORMATE ACETYLTRANSFERASE 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

FORMATE ACETYLTRANSFERASE 1

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