SMTL ID : 1q6y.1

Hypothetical protein YfdW from E. coli bound to Coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x COA: COENZYME A(Non-covalent)

COA.1: 25 residues within 4Å: Chain A: F.15, V.18, Q.19, S.20, E.39, R.40, L.74, N.75, T.76, K.77, N.98, F.99, H.100, A.103, M.107, I.126, K.127, G.128, K.139, A.140, Y.141, D.171, M.202 Chain B: Q.275, Q.277 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.139, A:Y.141 Hydrogen bonds: A:S.20, A:L.74, A:T.76, A:N.98, A:N.98, A:H.100, A:A.140, A:A.140, B:Q.275, B:Q.277 Water bridges: A:R.40, A:R.40, A:R.40, A:R.40, A:R.40, A:R.40 Salt bridges: A:R.40, A:K.77, A:H.100, A:H.100, A:K.139 pi-Stacking: A:F.99 pi-Cation interactions: A:R.40 COA.9: 25 residues within 4Å: Chain A: Q.275, Q.277 Chain B: F.15, V.18, Q.19, S.20, E.39, R.40, L.74, N.75, T.76, K.77, N.98, F.99, H.100, A.103, M.107, I.126, K.127, G.128, K.139, A.140, Y.141, D.171, M.202 25 PLIP interactions: 23 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.139, B:Y.141 Hydrogen bonds: B:S.20, B:L.74, B:T.76, B:N.98, B:N.98, B:H.100, B:A.140, B:A.140, A:Q.275, A:Q.277 Water bridges: B:R.40, B:R.40, B:R.40, B:R.40, B:R.40, B:R.40 Salt bridges: B:R.40, B:K.77, B:H.100, B:H.100, B:K.139 pi-Stacking: B:F.99 pi-Cation interactions: B:R.40

14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 9 residues within 4Å: Chain A: W.262, E.263, T.264, D.265, P.266, Y.269 Chain B: W.158, G.160, R.243 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.262 Hydrogen bonds: A:Y.269 MPD.3: 3 residues within 4Å: Chain A: A.285, I.286, Y.317 No protein-ligand interaction detected (PLIP) MPD.4: 4 residues within 4Å: Chain A: P.134 Chain B: V.327, A.328, T.331 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.134 MPD.5: 8 residues within 4Å: Chain A: T.5, A.29, W.30, G.32, N.68, P.383, D.384, K.386 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.384 Hydrogen bonds: A:W.30 MPD.6: 5 residues within 4Å: Chain A: Q.218, D.221 Chain B: K.368, Y.369, L.370 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.368, B:L.370, A:Q.218 MPD.7: 5 residues within 4Å: Chain A: W.158, P.230, Q.231, N.234, G.235 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.158, A:Q.231 Water bridges: A:P.230, A:N.234, A:G.235 MPD.8: 7 residues within 4Å: Chain A: P.41, E.73, L.74, T.395, M.412, K.413, H.416 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.73, A:T.395, A:H.416 Water bridges: A:E.73, A:N.75 MPD.10: 9 residues within 4Å: Chain A: W.158, G.160, R.243 Chain B: W.262, E.263, T.264, D.265, P.266, Y.269 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.262 Hydrogen bonds: B:Y.269, B:Y.269 MPD.11: 3 residues within 4Å: Chain B: A.285, I.286, Y.317 No protein-ligand interaction detected (PLIP) MPD.12: 4 residues within 4Å: Chain A: V.327, A.328, T.331 Chain B: P.134 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.134 MPD.13: 8 residues within 4Å: Chain B: T.5, A.29, W.30, G.32, N.68, P.383, D.384, K.386 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.384 Hydrogen bonds: B:W.30 MPD.14: 5 residues within 4Å: Chain A: K.368, Y.369, L.370 Chain B: Q.218, D.221 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.218, A:K.368, A:L.370 Hydrogen bonds: B:D.221 MPD.15: 5 residues within 4Å: Chain B: W.158, P.230, Q.231, N.234, G.235 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.158, B:Q.231 Water bridges: B:P.230, B:N.234, B:G.235 MPD.16: 7 residues within 4Å: Chain B: P.41, E.73, L.74, T.395, M.412, K.413, H.416 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.73, B:T.395, B:H.416 Water bridges: B:E.73, B:E.73, B:N.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gogos, A. et al., Structure of Escherichia coli YfdW, a type III CoA transferase. Acta Crystallogr.,Sect.D (2004)

Release Date

2003-09-30

Peptides

Hypothetical protein yfdW: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypothetical protein yfdW

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