SMTL ID : 2zxh.1

Structure of Aquifex aeolicus GidA in the form I crystal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 32 residues within 4Å: Chain A: I.33, G.34, G.35, G.36, H.37, A.38, V.57, L.58, S.67, C.68, K.77, E.144, E.145, V.146, T.175, T.176, G.177, T.178, F.179, R.195, S.201, T.220, G.221, T.222, Y.368, I.370, G.396, N.397, T.402, G.403, A.407, R.454 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.222, A:Y.368, A:I.370 Hydrogen bonds: A:G.35, A:G.36, A:H.37, A:A.38, A:L.58, A:K.77, A:V.146, A:V.146, A:T.178, A:T.178, A:S.201, A:T.220, A:N.397, A:N.397, A:T.402, A:G.403, A:R.454, A:R.454 Salt bridges: A:H.37, A:H.37, A:R.195 FAD.4: 35 residues within 4Å: Chain B: I.33, G.34, G.35, G.36, H.37, A.38, G.39, F.56, V.57, L.58, T.62, S.67, C.68, K.77, E.144, E.145, V.146, T.175, T.176, G.177, T.178, F.179, R.195, S.201, T.220, G.221, Y.368, I.370, G.396, N.397, T.402, G.403, Y.404, A.407, R.454 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:R.195, B:Y.368, B:I.370 Hydrogen bonds: B:G.35, B:G.36, B:H.37, B:A.38, B:G.39, B:L.58, B:K.77, B:V.146, B:V.146, B:T.178, B:R.195, B:S.201, B:N.397, B:N.397, B:G.403, B:R.454 Salt bridges: B:R.195

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

PO4.2: 4 residues within 4Å: Chain A: K.109, R.459 Chain B: K.297, D.316 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.316, A:R.463 Salt bridges: B:K.297, A:K.109, A:R.459 PO4.3: 3 residues within 4Å: Chain A: K.297, D.316 Chain B: R.459 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.297, B:R.459 PO4.5: 6 residues within 4Å: Chain B: P.301, R.302, K.317, R.319, H.320, Q.321 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.321 Salt bridges: B:R.302, B:K.310, B:K.317, B:H.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osawa, T. et al., Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Structure (2009)

Release Date

2009-05-19

Peptides

tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG

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