SMTL ID : 3i7s.1 (1 other biounit)

Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound in the active site.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.48, A.49, G.78, V.103, Y.106 Chain B: N.80, Y.107 Ligands: GOL.5 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.48, B:N.80, B:N.80 Water bridges: A:T.44, A:V.103, B:Y.107 GOL.2: 4 residues within 4Å: Chain A: K.174, E.175, L.176, V.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.174, A:L.176 GOL.5: 6 residues within 4Å: Chain A: A.49, Y.106 Chain B: N.80, Y.106 Ligands: GOL.1, K.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.49, A:Y.106 Water bridges: A:N.80 GOL.9: 6 residues within 4Å: Chain A: N.80, Y.107 Chain B: S.48, A.49, G.78, Y.106 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.80, A:N.80, B:S.48 Water bridges: B:G.78 GOL.10: 5 residues within 4Å: Chain B: D.29, V.32, A.33, R.70 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.29, B:A.33, B:R.70 GOL.13: 7 residues within 4Å: Chain B: P.110, S.111, Q.112, C.141, D.142, L.144 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.110, B:Q.112, B:D.142, B:D.142 GOL.16: 5 residues within 4Å: Chain B: K.26, D.29, A.33, L.261 Ligands: GOL.10 No protein-ligand interaction detected (PLIP) GOL.17: 4 residues within 4Å: Chain A: V.245 Chain B: S.111, Q.112 Ligands: GOL.13 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:V.245, B:Q.112 Water bridges: B:Q.112, B:Q.112, B:E.113

6 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: A.152, V.154, K.155, I.157 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.152, A:V.154, A:I.157 K.4: 4 residues within 4Å: Chain A: S.48, A.49, L.51 Ligands: GOL.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.48, A:L.51, H2O.3, H2O.3 K.11: 1 residues within 4Å: Chain B: H.125 No protein-ligand interaction detected (PLIP) K.12: 3 residues within 4Å: Chain B: S.48, A.49, L.51 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.51, H2O.7 K.14: 1 residues within 4Å: Chain B: E.84 No protein-ligand interaction detected (PLIP) K.15: 4 residues within 4Å: Chain B: A.152, V.154, K.155, I.157 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.152, B:V.154, B:I.157

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.6: 7 residues within 4Å: Chain A: A.8, G.43, T.44, T.45, L.101, Y.133, I.203 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.44, A:T.44, A:T.45 Water bridges: A:Y.133, B:Y.107 PYR.18: 8 residues within 4Å: Chain B: A.8, G.43, T.44, T.45, L.101, Y.133, I.203, V.205 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.44, B:T.44, B:T.45, B:T.45 Water bridges: B:Y.133, B:V.205

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

PO4.7: 2 residues within 4Å: Chain A: R.21, K.25 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.21 Salt bridges: A:R.21, A:K.25 PO4.8: 1 residues within 4Å: Chain A: R.109 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.109 PO4.19: 1 residues within 4Å: Chain B: R.109 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.109, B:R.109 Salt bridges: B:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soares da Costa, T.P. et al., How essential is the 'essential' active-site lysine in dihydrodipicolinate synthase?. Biochimie (2010)

Release Date

2010-04-14

Peptides

Dihydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrodipicolinate synthase

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