SMTL ID : 6gwj.1

Human OSGEP / LAGE3 / GON7 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: P.88, H.89, Q.90, R.91, V.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.89, A:Q.90, A:R.91, A:V.92 GOL.2: 3 residues within 4Å: Chain A: Q.135 Chain B: D.28, F.30 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.135 GOL.5: 7 residues within 4Å: Chain A: A.86, P.88 Chain C: G.83, A.84, V.87, V.320, Q.322 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.86, C:Q.322 Water bridges: A:D.85, A:D.85 GOL.6: 3 residues within 4Å: Chain C: R.308, A.309, W.333 5 PLIP interactions: 5 interactions with chain C Water bridges: C:E.305, C:R.308, C:R.308, C:R.308, C:R.308 GOL.7: 9 residues within 4Å: Chain C: N.12, K.13, T.31, Y.32, V.33, N.172, P.174, S.175, P.176 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.12 Water bridges: C:Y.32, C:D.162, C:S.175

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 3 residues within 4Å: Chain C: E.143, H.144, D.335 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.143, C:D.335

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain C: H.109, H.113, Y.130, D.294 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.113, C:D.294, H2O.3, H2O.5

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 5 residues within 4Å: Chain C: G.22, K.23, V.24, L.119, I.120 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.24, C:V.24, C:L.119 PEG.9: 5 residues within 4Å: Chain A: L.73, E.76, R.143 Chain C: Q.98, L.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.143 Water bridges: A:E.76 PEG.10: 9 residues within 4Å: Chain C: K.78, G.106, M.306, H.311, R.312, T.313, P.314, D.317, Y.324 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.311, C:D.317 Water bridges: C:Y.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arrondel, C. et al., Defects in t 6 A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome. Nat Commun (2019)

Release Date

2019-07-03

Peptides

EKC/KEOPS complex subunit LAGE3: A
EKC/KEOPS complex subunit GON7: B
Probable tRNA N6-adenosine threonylcarbamoyltransferase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
K

EKC/KEOPS complex subunit LAGE3

EKC/KEOPS complex subunit GON7

Probable tRNA N6-adenosine threonylcarbamoyltransferase