SMTL ID : 3fa3.4 (3 other biounits)

Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: A.47, D.86, D.88, K.121 Ligands: OAF.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.86, H2O.1, H2O.1, H2O.1 MN.4: 4 residues within 4Å: Chain B: G.46, D.58, D.86, D.88 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.86, B:D.88, H2O.2, H2O.2, H2O.2 MN.5: 7 residues within 4Å: Chain C: G.46, D.58, D.86, D.88, K.121, R.160 Ligands: OAF.6 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.86, H2O.3, H2O.3, H2O.3 MN.7: 6 residues within 4Å: Chain D: G.46, D.58, D.86, D.88, K.121 Ligands: OAF.8 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.86, H2O.4, H2O.4, H2O.4

3 x OAF: 2,2-difluoro-3,3-dihydroxybutanedioic acid(Non-covalent)

OAF.2: 15 residues within 4Å: Chain A: Y.43, T.45, G.46, A.47, D.58, D.86, C.123, G.124, H.125, R.160, E.190, N.213, V.215, P.239 Ligands: MN.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.43, A:T.45, A:G.46, A:A.47, A:D.86, A:G.124, A:R.160, A:R.160, A:N.213 Water bridges: A:K.121, A:K.121, A:K.121 Salt bridges: A:R.160 Halogen bonds: A:D.58 OAF.6: 15 residues within 4Å: Chain C: Y.43, T.45, G.46, A.47, D.58, D.86, C.123, G.124, H.125, R.160, E.190, N.213, V.215, P.239 Ligands: MN.5 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.43, C:T.45, C:G.46, C:A.47, C:D.58, C:G.124, C:R.160, C:E.190, C:N.213 Water bridges: C:R.160, C:R.160 Salt bridges: C:R.160 Halogen bonds: C:D.58 OAF.8: 15 residues within 4Å: Chain D: Y.43, T.45, G.46, A.47, D.58, D.86, C.123, G.124, H.125, R.160, E.190, N.213, V.215, P.239 Ligands: MN.7 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.43, D:Y.43, D:G.46, D:A.47, D:G.124, D:R.160, D:R.160, D:N.213 Water bridges: D:D.58, D:D.58, D:K.121 Salt bridges: D:H.125, D:R.160

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Q.289, A.294, G.297, G.298 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Narayanan, B. et al., Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member. J.Mol.Biol. (2009)

Release Date

2009-01-27

Peptides

2,3-dimethylmalate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
O

D
P

2,3-dimethylmalate lyase

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