SMTL ID : 1jrk.3 (2 other biounits)

Crystal Structure of a Nudix Protein from Pyrobaculum aerophilum Reveals a Dimer with Intertwined Beta Sheets

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 6 residues within 4Å: Chain A: F.59, T.60, Y.61, I.142 Chain C: I.142 Ligands: MPD.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.61, A:Y.61, C:I.142 MPD.2: 7 residues within 4Å: Chain B: L.8, V.9, E.10, V.98, K.99, R.100 Chain D: L.149 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.8, B:E.10, B:K.99 Hydrogen bonds: B:E.10, B:V.98, B:R.100 Water bridges: B:V.98 MPD.3: 7 residues within 4Å: Chain A: Y.61 Chain B: G.58, F.59, M.73, P.74, L.75 Ligands: MPD.1 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.75 Hydrogen bonds: B:F.59, B:M.73 Water bridges: B:I.57, B:M.73 MPD.4: 8 residues within 4Å: Chain A: L.145 Chain C: G.58, F.59, M.73, P.74, L.75 Chain D: Y.61, M.73 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:L.145 Hydrogen bonds: C:F.59, C:L.75, D:Y.61 MPD.5: 7 residues within 4Å: Chain C: K.18, H.19, K.20, G.29, G.30, E.49, H.91 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.20, C:K.20 Hydrogen bonds: C:G.29 MPD.6: 5 residues within 4Å: Chain C: E.10, N.11, K.13, R.100, W.110 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:K.13, C:W.110, C:W.110, C:W.110 Hydrogen bonds: C:E.10, C:N.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets. Acta Crystallogr.,Sect.D (2002)

Release Date

2002-04-03

Peptides

Nudix homolog: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nudix homolog

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