SMTL ID : 1k2e.1

crystal structure of a nudix protein from Pyrobaculum aerophilum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.124, V.125, R.126, K.127 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.124, A:R.126, A:K.127 Water bridges: A:V.125, A:V.125, A:K.127 Salt bridges: A:R.126, A:K.127 SO4.2: 5 residues within 4Å: Chain B: P.123, N.124, V.125, R.126, K.127 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.121, B:N.124, B:R.126, B:K.127 Water bridges: B:V.125 Salt bridges: B:R.126

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

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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: V.3, H.19, I.26, G.29, G.30, E.80, H.91, D.93 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.19, A:G.29, A:D.93 GOL.6: 9 residues within 4Å: Chain A: V.17, K.18, H.19, K.20, I.26, G.29, G.30, E.49 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.18, A:K.20, A:K.20, A:K.20 GOL.7: 5 residues within 4Å: Chain B: H.19, I.26, E.80, H.91, D.93 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.80, B:H.91 GOL.8: 3 residues within 4Å: Chain A: S.134, Y.137, R.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.138, A:R.138 Water bridges: A:S.134 GOL.9: 6 residues within 4Å: Chain A: N.35 Chain B: M.1, T.88, H.89, I.90, H.91 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.1, B:I.90, B:H.91, A:N.35 GOL.10: 4 residues within 4Å: Chain B: E.10, N.11, R.100, W.110 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.10, B:N.11, B:R.100 Water bridges: B:W.110

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

ACY.11: 10 residues within 4Å: Chain B: Y.27, L.78, E.80, D.93, I.95, F.122, P.123, N.124, V.125, V.128 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.78, B:N.124, B:V.128 Hydrogen bonds: B:N.124 ACY.12: 3 residues within 4Å: Chain A: V.81, V.82, K.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.83

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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