SMTL ID : 4ywj.1

Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 21 residues within 4Å: Chain A: V.15, G.16, A.18, G.19, R.20, M.21, D.43, R.44, F.84, T.85, V.89, G.107, T.108, T.109, A.131, A.132, N.133, F.134, R.245, F.248 Ligands: PGE.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.248 Hydrogen bonds: A:G.16, A:A.18, A:R.20, A:M.21, A:T.85, A:G.107, A:T.109, A:F.134 Water bridges: A:G.22, A:D.43, A:R.245, A:R.245 Salt bridges: A:R.20, A:R.20, A:R.245 pi-Stacking: A:F.84 NAD.5: 20 residues within 4Å: Chain B: V.15, G.16, A.18, G.19, R.20, M.21, D.43, R.44, F.84, T.85, V.89, G.107, T.108, T.109, A.131, A.132, N.133, F.134, F.248 Ligands: PGE.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.84, B:F.248 Hydrogen bonds: B:G.16, B:A.18, B:R.20, B:M.21, B:T.85, B:G.107, B:T.109, B:F.134 Water bridges: B:G.22 Salt bridges: B:R.20, B:R.20 NAD.8: 21 residues within 4Å: Chain C: V.15, G.16, A.18, G.19, R.20, M.21, D.43, R.44, F.84, T.85, V.89, G.107, T.108, T.109, A.131, A.132, N.133, F.134, R.245, F.248 Ligands: PGE.9 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.248 Hydrogen bonds: C:G.16, C:A.18, C:R.20, C:M.21, C:T.85, C:G.107, C:T.109, C:F.134 Water bridges: C:G.22, C:D.43, C:R.245, C:R.245 Salt bridges: C:R.20, C:R.20, C:R.245 pi-Stacking: C:F.84 NAD.12: 20 residues within 4Å: Chain D: V.15, G.16, A.18, G.19, R.20, M.21, D.43, R.44, F.84, T.85, V.89, G.107, T.108, T.109, A.131, A.132, N.133, F.134, F.248 Ligands: PGE.13 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.84, D:F.248 Hydrogen bonds: D:G.16, D:A.18, D:R.20, D:M.21, D:T.85, D:G.107, D:T.109, D:F.134 Water bridges: D:G.22 Salt bridges: D:R.20, D:R.20

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 5 residues within 4Å: Chain A: T.109, A.132, N.133, F.248 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.133, A:T.175, A:R.245 PGE.6: 5 residues within 4Å: Chain B: T.109, A.132, N.133, F.248 Ligands: NAD.5 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.175, B:T.175, B:T.175 PGE.9: 5 residues within 4Å: Chain C: T.109, A.132, N.133, F.248 Ligands: NAD.8 3 PLIP interactions: 3 interactions with chain C Water bridges: C:T.175, C:T.175, C:R.245 PGE.13: 5 residues within 4Å: Chain D: T.109, A.132, N.133, F.248 Ligands: NAD.12 4 PLIP interactions: 4 interactions with chain D Water bridges: D:N.133, D:T.175, D:T.175, D:T.175

4 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.3: 5 residues within 4Å: Chain A: I.161, E.162, A.163, D.224, T.226 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:I.161, A:A.163, A:D.224 Hydrogen bonds: A:T.226 Water bridges: C:K.241, C:K.241, C:K.241 BU1.7: 6 residues within 4Å: Chain B: I.161, E.162, D.224, H.225, T.226 Chain C: E.237 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 interactions with chain B Water bridges: D:K.241, C:R.235 Hydrogen bonds: C:E.237, B:T.226 Hydrophobic interactions: B:I.161 BU1.10: 5 residues within 4Å: Chain C: I.161, E.162, A.163, D.224, T.226 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.161, C:A.163, C:D.224 Hydrogen bonds: C:T.226, C:T.226 Water bridges: A:K.241, A:K.241, A:K.241 BU1.14: 6 residues within 4Å: Chain A: E.237 Chain D: I.161, E.162, D.224, H.225, T.226 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: A:E.237, D:T.226, D:T.226 Water bridges: A:R.235, B:K.241 Hydrophobic interactions: D:I.161

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

CL.4: 2 residues within 4Å: Chain A: T.147 Chain B: T.147 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain C: T.147 Chain D: T.147 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from Pseudomonas aeruginosa. to be published

Release Date

2015-04-01

Peptides

4-hydroxy-tetrahydrodipicolinate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

4-hydroxy-tetrahydrodipicolinate reductase