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

The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: P.96, C.99, A.100, N.103, D.104, L.106, Y.108, G.181, Q.182, V.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.104 Water bridges: A:P.96, A:G.181 GOL.2: 3 residues within 4Å: Chain A: R.203, T.209, D.210 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.203, A:D.210, A:D.210 Water bridges: A:T.211 GOL.5: 10 residues within 4Å: Chain B: P.96, C.99, A.100, N.103, D.104, L.106, Y.108, G.181, Q.182, V.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.104, B:L.106 Water bridges: B:G.181

2 x MC4: 2-METHYLACETOACETYL COA(Non-covalent)

MC4.3: 26 residues within 4Å: Chain A: I.16, G.17, P.18, D.37, R.38, A.59, D.60, L.61, K.62, G.83, Y.84, R.85, V.88, R.91, L.92, G.113, A.124, G.125, H.126, D.127, Y.130, D.156 Chain B: L.217, Y.224, I.240, F.244 25 PLIP interactions: 22 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.124, A:H.126, B:F.244 Hydrogen bonds: A:R.38, A:R.38, A:A.59, A:D.60, A:L.61, A:K.62, A:G.83, A:G.83, A:R.85, A:H.126, A:D.127, A:Y.130 Water bridges: A:Y.84, A:R.91, A:R.91, B:Q.243, B:Q.243 Salt bridges: A:K.62, A:R.85, A:R.85, A:R.91 pi-Cation interactions: A:R.38 MC4.6: 26 residues within 4Å: Chain A: L.217, Y.224, I.240, F.244 Chain B: I.16, G.17, P.18, D.37, R.38, A.59, D.60, L.61, K.62, G.83, Y.84, R.85, V.88, R.91, L.92, G.113, A.124, G.125, H.126, D.127, Y.130, D.156 27 PLIP interactions: 23 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.16, B:A.124, B:H.126, A:L.217, A:F.244 Hydrogen bonds: B:R.38, B:A.59, B:L.61, B:G.83, B:G.83, B:R.85, B:D.127, B:Y.130, B:Y.130 Water bridges: B:I.16, B:K.62, B:Y.84, B:R.85, B:R.91, B:R.91, A:Q.243, A:Q.243 Salt bridges: B:K.62, B:R.85, B:R.85, B:R.91 pi-Cation interactions: B:R.38

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 1 residues within 4Å: Chain B: H.282 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.281, B:S.281, B:S.281 Salt bridges: B:H.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, S. et al., The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed Qm/Mm Calculations. J Phys Chem B (2012)

Release Date

2012-03-28

Peptides

PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE ): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

PROBABLE ALPHA-METHYLACYL-COA RACEMASE MCR (2-METHYLACYL-COA RACEMASE) (2-ARYLPROPIONYL-COA EPIMERASE )

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