SMTL ID : 1h18.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.1: 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.272, A:F.327, A:W.333 Water bridges: A:C.419 Salt bridges: A:R.176, A:R.435 PYR.10: 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 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.272, B:F.327, B:W.333 Water bridges: B:C.419 Salt bridges: B:R.176, B:R.435

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

NA.2: 4 residues within 4Å: Chain A: A.652, L.654, E.700, G.701 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.654, A:E.700 NA.3: 4 residues within 4Å: Chain A: Y.499 Chain B: E.214, Q.215, R.218 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.218, A:Y.499 Water bridges: B:R.218 NA.4: 2 residues within 4Å: Chain A: G.687, L.688 No protein-ligand interaction detected (PLIP) NA.11: 5 residues within 4Å: Chain B: A.652, L.654, F.656, E.700, G.701 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.656, B:E.700, B:G.701 Water bridges: B:Q.703 NA.12: 3 residues within 4Å: Chain B: T.80, I.81, Q.232 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.81 Water bridges: B:S.79, B:T.80, B:T.82, B:Q.232 NA.13: 1 residues within 4Å: Chain B: K.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.62, B:K.62 NA.14: 1 residues within 4Å: Chain A: F.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.141

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

DTL.5: 8 residues within 4Å: Chain A: E.225, R.228, Q.232 Chain B: T.138, E.139, Y.140, K.142, Q.146 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Water bridges: B:T.138, B:Y.140, B:R.141, B:K.142, B:Q.146, A:R.228 Hydrogen bonds: A:R.228, A:Q.232 DTL.6: 8 residues within 4Å: Chain A: H.68, A.69, P.70, R.107, Y.125, D.324, D.330, S.741 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.125, A:D.324 Water bridges: A:R.107, A:R.107, A:R.319, A:D.324, A:G.329 DTL.15: 6 residues within 4Å: Chain A: T.138, E.139, K.142 Chain B: E.225, R.228, Q.232 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:E.139, A:R.141, B:R.228 Hydrogen bonds: B:R.228, B:Q.232 DTL.16: 7 residues within 4Å: Chain B: H.68, A.69, P.70, Y.125, D.324, D.330, S.741 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.125, B:Y.125, B:D.324, B:D.330 Water bridges: B:N.65, B:R.107, B:R.107, B:R.107, B:G.329

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

PG4.7: 4 residues within 4Å: Chain A: E.40, S.41, L.43, Y.361 No protein-ligand interaction detected (PLIP) PG4.8: 1 residues within 4Å: Chain A: A.238 No protein-ligand interaction detected (PLIP) PG4.9: 6 residues within 4Å: Chain A: V.645, L.648, T.649, L.688, G.691, Y.692 No protein-ligand interaction detected (PLIP) PG4.17: 4 residues within 4Å: Chain B: E.40, L.43, N.358, Y.361 No protein-ligand interaction detected (PLIP) PG4.18: 5 residues within 4Å: Chain B: V.645, T.649, L.688, G.691, Y.692 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
B

FORMATE ACETYLTRANSFERASE 1

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