SMTL ID : 3ijp.1

Crystal structure of dihydrodipicolinate reductase from bartonella henselae at 2.0A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: I.41, R.44, V.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.44 NA.8: 3 residues within 4Å: Chain B: I.41, R.44, V.47 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.41 Water bridges: B:Q.42 NA.10: 3 residues within 4Å: Chain C: I.41, R.44, V.47 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.47 NA.17: 3 residues within 4Å: Chain D: I.41, R.44, V.47 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.41 Water bridges: D:Q.42

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: H.176, K.179 Ligands: NAP.3, UNX.5 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: G.28, A.29, N.30, V.54, R.55 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain C: H.176, K.179 Ligands: NAP.12, UNX.14 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain D: G.28, A.29, N.30, V.54, R.55 Ligand excluded by PLIP

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.3: 25 residues within 4Å: Chain A: G.28, A.29, N.30, G.31, R.32, M.33, R.55, F.95, S.96, Q.97, A.100, Y.104, G.118, T.119, T.120, S.142, G.143, N.144, M.145, K.179, D.181, F.259 Ligands: CL.2, UNX.5, UNX.7 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:F.259 Hydrogen bonds: A:G.28, A:N.30, A:N.30, A:N.30, A:G.31, A:R.32, A:M.33, A:R.55, A:R.55, A:G.118, A:T.120, A:M.145, A:D.181 Water bridges: A:R.32, A:R.32, A:R.32, A:R.32, A:R.32, A:G.34, A:T.120, A:T.120, A:R.256 Salt bridges: A:R.32, A:R.32, A:R.55 pi-Stacking: A:F.95, A:F.259 pi-Cation interactions: A:R.55, A:R.55 NAP.12: 25 residues within 4Å: Chain C: G.28, A.29, N.30, G.31, R.32, M.33, R.55, F.95, S.96, Q.97, A.100, Y.104, G.118, T.119, T.120, S.142, G.143, N.144, M.145, K.179, D.181, F.259 Ligands: CL.11, UNX.14, UNX.16 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:F.259 Hydrogen bonds: C:G.28, C:N.30, C:N.30, C:N.30, C:G.31, C:R.32, C:M.33, C:R.55, C:R.55, C:Y.104, C:G.118, C:T.120, C:M.145, C:D.181 Water bridges: C:R.32, C:R.32, C:R.32, C:R.32, C:R.32, C:G.34, C:R.256 Salt bridges: C:R.32, C:R.32, C:R.55 pi-Stacking: C:F.95, C:F.259 pi-Cation interactions: C:R.55, C:R.55

8 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 5 residues within 4Å: Chain A: H.175, I.233, G.234, F.259 Ligands: UNX.5 No protein-ligand interaction detected (PLIP) UNX.5: 4 residues within 4Å: Ligands: CL.2, NAP.3, UNX.4, UNX.6 No protein-ligand interaction detected (PLIP) UNX.6: 4 residues within 4Å: Chain A: G.143, T.186 Ligands: UNX.5, UNX.7 No protein-ligand interaction detected (PLIP) UNX.7: 7 residues within 4Å: Chain A: T.120, K.179, D.181, S.184, G.185 Ligands: NAP.3, UNX.6 No protein-ligand interaction detected (PLIP) UNX.13: 5 residues within 4Å: Chain C: H.175, I.233, G.234, F.259 Ligands: UNX.14 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Ligands: CL.11, NAP.12, UNX.13, UNX.15 No protein-ligand interaction detected (PLIP) UNX.15: 4 residues within 4Å: Chain C: G.143, T.186 Ligands: UNX.14, UNX.16 No protein-ligand interaction detected (PLIP) UNX.16: 7 residues within 4Å: Chain C: T.120, K.179, D.181, S.184, G.185 Ligands: NAP.12, UNX.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cala, A.R. et al., The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 angstrom resolution. Acta Crystallogr F Struct Biol Commun (2016)

Release Date

2009-08-11

Peptides

Dihydrodipicolinate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Dihydrodipicolinate reductase