SMTL ID : 5y7d.1

Crystal structure of human Endothelial-overexpressed LPS associated factor 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: F.9, R.10, Y.13, E.25, T.26, W.49, L.114 Ligands: NA.3, NA.4, NA.5, CL.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.10, A:R.10 Water bridges: A:E.25, A:R.27, A:R.27, A:R.27 GOL.2: 5 residues within 4Å: Chain A: P.30, L.31, S.33, S.34, V.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.30, A:S.33, A:S.34, A:S.34 GOL.17: 11 residues within 4Å: Chain B: F.9, R.10, Y.13, E.25, T.26, W.49, L.114 Ligands: NA.19, NA.20, NA.21, CL.28 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.10, B:R.10 Water bridges: B:E.25, B:R.27, B:R.27, B:R.27 GOL.18: 5 residues within 4Å: Chain B: P.30, L.31, S.33, S.34, V.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.30, B:S.33, B:S.34, B:S.34

10 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: E.25, T.26, R.27 Ligands: GOL.1, NA.4, NA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.26 Water bridges: A:R.27 NA.4: 6 residues within 4Å: Chain A: K.22, E.25, T.26, L.114 Ligands: GOL.1, NA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.22, A:T.26, A:T.26 NA.5: 6 residues within 4Å: Chain A: T.26, W.28, K.120 Ligands: GOL.1, NA.3, NA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.26, A:K.120 NA.6: 4 residues within 4Å: Chain A: R.27, W.28 Ligands: NA.5, NA.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.28 NA.7: 5 residues within 4Å: Chain A: R.27, W.28, R.29, L.31 Ligands: NA.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.27, A:W.28, A:R.29, A:R.29 NA.19: 6 residues within 4Å: Chain B: E.25, T.26, R.27 Ligands: GOL.17, NA.20, NA.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.26 Water bridges: B:R.27 NA.20: 6 residues within 4Å: Chain B: K.22, E.25, T.26, L.114 Ligands: GOL.17, NA.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.22, B:T.26, B:T.26 NA.21: 6 residues within 4Å: Chain B: T.26, W.28, K.120 Ligands: GOL.17, NA.19, NA.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.28, B:K.120 NA.22: 4 residues within 4Å: Chain B: R.27, W.28 Ligands: NA.21, NA.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.28 Water bridges: B:R.27 NA.23: 5 residues within 4Å: Chain B: R.27, W.28, R.29, L.31 Ligands: NA.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.28, B:R.29, B:R.29, B:R.29

18 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: R.137, G.140, F.144 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: W.49, G.51, D.52, L.114 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: R.36, N.37 Chain B: L.87, R.129, I.153 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: R.137, V.146, D.147 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: R.10, W.49 Ligands: GOL.1 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: R.10, A.45, H.46, R.47 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: P.30, L.31 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: R.129, W.130 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: K.3 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: R.137, G.140, F.144 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain B: W.49, G.51, D.52, L.114 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain A: L.87, R.129, I.153 Chain B: R.36, N.37 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: R.137, V.146, D.147 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: R.10, W.49 Ligands: GOL.17 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: R.10, A.45, H.46, R.47 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: P.30, L.31 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain B: R.129, W.130 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Chain B: K.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, M. et al., Crystal Structure of Human EOLA1 Implies Its Possibility of RNA Binding. Molecules (2019)

Release Date

2018-08-22

Peptides

Protein CXorf40A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein CXorf40A