SMTL ID : 6ra9.1

Novel structural features and post-translational modifications in eukaryotic elongation factor 1A2 from Oryctolagus cuniculus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

3 x GPE: L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE(Covalent)

GPE.1: 2 residues within 4Å: Chain A: A.373, E.374 No protein-ligand interaction detected (PLIP) GPE.2: 3 residues within 4Å: Chain A: T.242, E.301, L.303 No protein-ligand interaction detected (PLIP) GPE.11: 2 residues within 4Å: Chain B: A.373, E.374 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.373, B:E.374

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 16 residues within 4Å: Chain A: H.15, V.16, D.17, S.18, G.19, K.20, S.21, T.22, S.53, N.153, K.154, D.156, S.157, S.194, G.195, W.196 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.17, A:D.17, A:S.18, A:G.19, A:K.20, A:S.21, A:T.22, A:T.22, A:S.53, A:N.153, A:K.154, A:K.154, A:S.157, A:S.157, A:G.195, A:W.196 Water bridges: A:T.22, A:S.53, A:S.53 Salt bridges: A:K.20, A:K.64, A:D.156 GDP.12: 15 residues within 4Å: Chain B: H.15, V.16, D.17, S.18, G.19, K.20, S.21, T.22, N.153, K.154, D.156, S.194, G.195, W.196 Ligands: GOL.13 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:H.15, B:D.17, B:S.18, B:G.19, B:G.19, B:K.20, B:S.21, B:T.22, B:T.22, B:N.153, B:K.154, B:K.154, B:S.194, B:G.195, B:W.196 Water bridges: B:K.20, B:K.20 Salt bridges: B:K.20, B:D.156

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: H.349, G.351, K.395, S.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.351, A:S.396 GOL.5: 1 residues within 4Å: Chain A: S.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.316, A:V.317 GOL.13: 3 residues within 4Å: Chain B: W.196, H.197 Ligands: GDP.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.197 GOL.14: 8 residues within 4Å: Chain B: K.146, Q.147, L.148, I.149, T.187, P.189, R.218, T.234 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.148, B:L.148, B:T.234, B:T.234 GOL.15: 7 residues within 4Å: Chain B: Y.167, P.185, V.188, P.189, F.190, W.214, K.215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.185, B:V.188, B:F.190, B:K.215 GOL.16: 5 residues within 4Å: Chain A: V.253, Y.254, K.255 Chain B: D.35, K.36 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.255, B:K.36

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

SO4.6: 3 residues within 4Å: Chain A: D.380, R.381, R.382 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.381, A:R.382 SO4.7: 6 residues within 4Å: Chain A: H.15, S.128, N.130, G.131, Q.132 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.128, A:Q.132, A:Q.132 Salt bridges: A:H.15 SO4.8: 3 residues within 4Å: Chain A: R.69, R.381 Chain B: R.69 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.69, A:R.69, A:R.381 SO4.9: 4 residues within 4Å: Chain A: P.160, S.163, E.164, K.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.164, A:K.165 SO4.10: 8 residues within 4Å: Chain A: H.15, G.126, I.127, S.128, G.131, Q.132, T.133 Ligands: SO4.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.128, A:S.128, A:Q.132, A:T.133, A:T.133 Salt bridges: A:H.15 SO4.17: 3 residues within 4Å: Chain B: R.96, N.348, R.381 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.348 Water bridges: B:R.381 Salt bridges: B:R.96, B:R.381 SO4.18: 4 residues within 4Å: Chain A: L.347, N.348 Chain B: R.69, R.96 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.69, B:R.96 Hydrogen bonds: A:N.348, A:N.348 SO4.19: 3 residues within 4Å: Chain B: K.129, R.134, Y.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.129, B:Y.177 Salt bridges: B:R.134 SO4.20: 4 residues within 4Å: Chain B: P.160, S.163, E.164, K.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.164, B:K.165 SO4.21: 4 residues within 4Å: Chain B: Y.141, K.146, S.416, Q.417 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.141, B:S.416, B:S.416, B:Q.417 Salt bridges: B:K.146 SO4.22: 2 residues within 4Å: Chain B: R.96, R.381 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.397 Salt bridges: B:R.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carriles, A.A. et al., Structural Cues for Understanding eEF1A2 Moonlighting. Chembiochem (2021)

Release Date

2020-06-03

Peptides

Elongation factor 1-alpha 2: A
Elongation factor 1-alpha 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Elongation factor 1-alpha 2

Elongation factor 1-alpha 2