SMTL ID : 3qy9.1

The Crystal Structure of Dihydrodipicolinate reductase from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

22 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: H.139, K.142, K.216 Ligands: SO4.3 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: K.142, S.147, G.148, T.149 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: K.142, V.143, D.144 Ligands: SO4.1 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: A.13, R.17, K.216 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain B: R.17 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: A.13, R.17, K.216 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: V.167, Y.168, D.169, L.173 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain B: H.138, H.139, K.142, K.216 Ligands: ACT.6 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain B: S.106, A.107, N.108, H.114, K.152, F.240 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: T.165, Q.180 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain C: R.17, S.215 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain C: K.142, S.147, G.148, T.149 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain C: K.141, K.142, V.143, D.144 Ligands: SO4.17 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain C: H.139, K.216 Ligands: SO4.16 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: A.13, R.17, K.216 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: G.12, A.13 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain D: K.142, S.147, G.148, T.149 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain D: H.139, K.142, K.216 Ligands: SO4.24 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain D: A.13, R.17, K.216 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain D: K.141, K.142, V.143, D.144 Ligands: SO4.22 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain D: G.12, A.13 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain D: N.100, N.235 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.17, S.215, K.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:K.216 GOL.13: 6 residues within 4Å: Chain B: T.84, K.142, D.144, S.147, G.148, T.149 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.148, B:T.149, B:T.149 Water bridges: B:T.149, B:H.196

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 5 residues within 4Å: Chain B: K.141, K.142, V.143, D.144 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.143 Hydrogen bonds: B:D.144, B:D.144 Salt bridges: B:K.142 ACT.20: 7 residues within 4Å: Chain D: S.62, N.63, P.64, L.67, T.83, E.86, L.90 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.67, D:L.90 Hydrogen bonds: D:S.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Girish, T.S. et al., Structure and nucleotide specificity of Staphylococcus aureus dihydrodipicolinate reductase (DapB). Febs Lett. (2011)

Release Date

2011-08-03

Peptides

Dihydrodipicolinate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dihydrodipicolinate reductase