SMTL ID : 3ngs.1

Structure of Leishmania nucleoside diphosphate kinase b with ordered nucleotide-binding loop

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: K.11, Y.51, R.104, N.114, C.116, H.117 Ligands: PO4.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.51, A:Y.51, A:N.114 Water bridges: A:K.11, A:K.11 Salt bridges: A:K.11, A:H.117 PO4.2: 6 residues within 4Å: Chain A: R.87, T.93, R.104, H.117, G.118 Ligands: PO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.118 Salt bridges: A:R.87, A:R.104, A:H.117 PO4.4: 7 residues within 4Å: Chain C: K.11, Y.51, T.93, R.104, N.114, C.116, H.117 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.51, C:N.114 Water bridges: C:K.11, C:Y.51, C:G.118 Salt bridges: C:K.11, C:R.104, C:H.117 PO4.5: 7 residues within 4Å: Chain D: K.11, Y.51, R.104, N.114, C.116, H.117 Ligands: PO4.6 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.51, D:N.114 Water bridges: D:K.11, D:K.11, D:H.117 Salt bridges: D:K.11, D:H.117 PO4.6: 6 residues within 4Å: Chain D: R.87, T.93, R.104, H.117, G.118 Ligands: PO4.5 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.118 Salt bridges: D:R.87, D:R.104, D:H.117 PO4.8: 7 residues within 4Å: Chain F: K.11, Y.51, T.93, R.104, N.114, C.116, H.117 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.114 Water bridges: F:K.11, F:Y.51, F:H.117, F:G.118 Salt bridges: F:K.11, F:R.104, F:H.117

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.3: 8 residues within 4Å: Chain B: K.11, H.50, Y.51, R.87, T.93, R.104, N.114, H.117 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.11, B:K.11, B:R.87, B:R.104, B:N.114, B:H.117 DTT.7: 8 residues within 4Å: Chain E: K.11, H.50, Y.51, R.87, T.93, R.104, N.114, H.117 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:K.11, E:K.11, E:R.87, E:R.104, E:N.114, E:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Souza, T.A. et al., Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding. Mol Biosyst (2011)

Release Date

2011-04-27

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Nucleoside diphosphate kinase

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