SMTL ID : 1k26.1

Structure of a Nudix Protein from Pyrobaculum aerophilum Solved by the Single Wavelength Anomolous Scattering Method

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: N.124, V.125, R.126, K.127 Ligands: IR3.12 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.124, A:R.126, A:K.127 Water bridges: A:T.121, A:V.125, A:R.126 Salt bridges: A:R.126, A:K.127 SO4.11: 5 residues within 4Å: Chain B: P.123, N.124, V.125, R.126, K.127 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.124, B:R.126, B:K.127 Water bridges: B:N.124, B:V.125, B:V.125 Salt bridges: B:K.127

4 x IR3: IRIDIUM (III) ION(Non-functional Binders)(Non-covalent)

IR3.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) IR3.3: 2 residues within 4Å: Chain A: E.66, N.67 No protein-ligand interaction detected (PLIP) IR3.4: 4 residues within 4Å: Chain A: K.20, H.31 Ligands: NI.5, GOL.8 No protein-ligand interaction detected (PLIP) IR3.12: 3 residues within 4Å: Chain B: D.65, E.66 Ligands: SO4.1 No protein-ligand interaction detected (PLIP)

2 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 5 residues within 4Å: Chain A: R.21, Y.84, H.89, H.91 Ligands: IR3.4 No protein-ligand interaction detected (PLIP) NI.13: 3 residues within 4Å: Chain B: H.31, Y.84, H.91 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: V.3, H.19, I.26, G.29, G.30, E.80, H.91, D.93 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.19, A:G.29, A:H.91, A:D.93 GOL.7: 3 residues within 4Å: Chain A: M.1, H.89, I.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.1, A:I.90 GOL.8: 8 residues within 4Å: Chain A: V.17, K.18, H.19, K.20, G.29, E.49 Ligands: IR3.4, GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.18, A:K.20

5 x ACY: ACETIC ACID(Non-functional Binders)

ACY.9: 5 residues within 4Å: Chain A: V.81, V.82, K.83, P.123 Chain B: N.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.83, A:K.83 ACY.10: 3 residues within 4Å: Chain A: E.10, N.11, W.110 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.110 Hydrogen bonds: A:E.10, A:N.11 ACY.14: 10 residues within 4Å: Chain B: S.5, Y.27, L.78, E.80, D.93, I.95, F.122, P.123, N.124, V.125 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.27, B:F.122, B:V.125 Hydrogen bonds: B:S.5, B:S.5 Water bridges: B:N.124 ACY.15: 3 residues within 4Å: Chain B: E.10, N.11, W.110 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.110 Hydrogen bonds: B:E.10, B:N.11 ACY.16: 4 residues within 4Å: Chain B: H.19, E.80, H.91, F.122 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.19, B:D.93 Salt bridges: B:H.91

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NUDIX HOMOLOG

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