SMTL ID : 6w3z.1

Crystal Structure of Brugia malayi Deoxyhypusine synthase (DHPS)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: T.102, S.103, N.104, L.105, S.129, A.130, G.131, D.236, G.280, G.281, N.305, T.306, G.307, A.339, D.340, A.341 Chain D: G.282, V.283, H.286, D.311, S.313, D.314, S.315 18 PLIP interactions: 7 interactions with chain D, 11 interactions with chain A Hydrogen bonds: D:G.282, D:D.314, D:D.314, D:S.315, D:S.315, D:S.315, D:S.315, A:S.103, A:N.104, A:S.129, A:S.129, A:A.130, A:G.131, A:D.236, A:G.281, A:T.306, A:D.340, A:A.341 NAD.3: 28 residues within 4Å: Chain B: T.102, S.103, N.104, L.105, T.107, S.129, A.130, G.131, E.134, D.236, G.237, G.280, G.281, N.305, T.306, G.307, A.339, D.340, A.341 Chain C: G.282, V.283, H.286, D.311, S.313, D.314, S.315, W.325 Ligands: NAD.6 25 PLIP interactions: 18 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:T.102, B:S.103, B:S.103, B:N.104, B:T.107, B:S.129, B:S.129, B:A.130, B:G.131, B:D.236, B:G.281, B:T.306, B:D.340, B:D.340, B:A.341, C:G.282, C:S.313, C:D.314, C:D.314, C:S.315, C:S.315, C:S.315 Water bridges: B:N.104, B:G.307, B:G.307 NAD.6: 29 residues within 4Å: Chain B: G.282, V.283, H.286, D.311, S.313, D.314, S.315 Chain C: T.102, S.103, N.104, L.105, T.107, S.129, A.130, G.131, E.134, E.135, D.236, G.280, G.281, V.304, N.305, T.306, G.307, S.315, A.339, D.340, A.341 Ligands: NAD.3 20 PLIP interactions: 8 interactions with chain B, 12 interactions with chain C Hydrogen bonds: B:G.282, B:S.313, B:D.314, B:D.314, B:D.314, B:S.315, B:S.315, B:S.315, C:S.103, C:N.104, C:S.129, C:S.129, C:A.130, C:G.131, C:G.281, C:T.306, C:T.306, C:D.340, C:A.341 Water bridges: C:V.283

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.111, E.112, K.139, P.143 Chain C: I.31, I.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.111, A:A.142 Water bridges: A:E.112, A:S.144 GOL.4: 8 residues within 4Å: Chain B: Y.116, A.354, V.357, Q.358 Chain D: F.37, N.38, G.40, I.41 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:I.41, B:Y.116 Water bridges: D:N.38, B:H.120 GOL.7: 6 residues within 4Å: Chain A: I.32, K.33 Chain C: R.111, E.112, K.139, P.143 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.111, C:A.142 Water bridges: C:S.144, C:R.216, C:R.216 GOL.8: 2 residues within 4Å: Chain D: E.15, M.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.16 GOL.9: 7 residues within 4Å: Chain B: I.31, I.32 Chain D: R.111, E.112, K.139, P.143, R.216 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.111, D:E.112 Water bridges: D:S.144, D:R.216

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

CL.5: 2 residues within 4Å: Chain B: F.197 Chain C: K.254 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva, S.F. et al., Structural features and development of an assay platform of the parasite target deoxyhypusine synthase of Brugia malayi and Leishmania major. Plos Negl Trop Dis (2020)

Release Date

2020-11-04

Peptides

BMA-DHPS-1, isoform a: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BMA-DHPS-1, isoform a