SMTL ID : 5di0.1

Crystal structure of Dln1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: V.56, H.124, T.126 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.82 EDO.2: 5 residues within 4Å: Chain A: L.27, I.29, V.147, M.160 Ligands: PEG.8 No protein-ligand interaction detected (PLIP) EDO.3: 7 residues within 4Å: Chain A: I.30, G.31, G.105, Y.134 Ligands: EDO.4, EDO.5, CL.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.31 Water bridges: A:Y.134 EDO.4: 8 residues within 4Å: Chain A: I.29, G.31, G.32, R.149, C.156 Ligands: EDO.3, EDO.5, PEG.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.29, A:G.31, A:R.149 Water bridges: A:R.149 EDO.5: 6 residues within 4Å: Chain A: G.31, G.32, Q.33, G.105 Ligands: EDO.3, EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.105 EDO.19: 5 residues within 4Å: Chain B: I.29, S.37, F.38, V.147, G.148 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.149 EDO.20: 7 residues within 4Å: Chain B: I.30, G.31, G.101, G.105, Y.134 Ligands: EDO.21, CL.35 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.31 EDO.21: 5 residues within 4Å: Chain B: I.29, G.31, G.32, Q.33 Ligands: EDO.20 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.31, B:G.31, B:Q.33 Water bridges: B:I.29, B:R.149 EDO.22: 1 residues within 4Å: Chain B: E.204 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.204 EDO.23: 4 residues within 4Å: Chain B: N.45, S.69, D.70, T.222 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.45, B:S.69 EDO.24: 1 residues within 4Å: Ligands: PG4.32 No protein-ligand interaction detected (PLIP) EDO.25: 3 residues within 4Å: Chain B: T.89, E.92, K.117 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.89 Water bridges: B:Y.86, B:E.92

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

PEG.6: 5 residues within 4Å: Chain A: S.36, F.38, F.76, G.77, G.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.74, A:G.77 PEG.7: 4 residues within 4Å: Chain A: G.58, W.59, S.127, W.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.58, A:S.127 PEG.8: 8 residues within 4Å: Chain A: I.29, S.37, F.38, V.147, G.148, R.149 Ligands: EDO.2, EDO.4 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: N.44, N.45, D.70, R.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.44, A:D.70 Water bridges: A:N.45, A:R.72 PEG.10: 7 residues within 4Å: Chain A: N.45, G.46, S.69, D.70, T.222, F.225, Y.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.222, A:Y.312, A:Y.312 PEG.11: 7 residues within 4Å: Chain A: T.187, E.242, F.247, T.286, I.287, G.288, K.327 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.286, A:I.287, A:K.327 Water bridges: A:T.324 PEG.26: 3 residues within 4Å: Chain B: T.25, N.26, L.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.25, B:L.27 Water bridges: B:N.26 PEG.27: 7 residues within 4Å: Chain B: T.187, E.242, F.247, T.286, I.287, G.288, K.327 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.286, B:T.286, B:K.327 Water bridges: B:T.187, B:T.324

7 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 3 residues within 4Å: Chain A: T.25, N.26, L.27 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.25, A:L.27 Water bridges: A:N.26, A:N.26, A:N.163, A:N.306 PGE.13: 5 residues within 4Å: Chain A: R.107, G.151, S.152, D.153, D.155 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.151, A:S.152, A:D.153, A:D.153 Water bridges: A:S.152 PGE.14: 5 residues within 4Å: Chain A: G.91, N.116, K.117 Chain B: E.188, K.211 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.116, A:K.117 Water bridges: B:R.289 PGE.15: 8 residues within 4Å: Chain A: F.122, H.124, M.125, T.126, S.127, W.128, G.129, L.130 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.129, A:L.130, A:L.130 PGE.28: 9 residues within 4Å: Chain B: S.36, S.37, F.38, E.74, T.75, F.76, G.77, G.150, G.151 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.74, B:G.77 Water bridges: B:T.75 PGE.29: 7 residues within 4Å: Chain B: F.122, H.124, M.125, T.126, S.127, W.128, L.130 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.130, B:L.130 PGE.30: 2 residues within 4Å: Chain B: W.59, W.128 No protein-ligand interaction detected (PLIP)

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.16: 6 residues within 4Å: Chain A: W.100, K.112, K.114, E.120, F.122, E.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.112, A:K.114, A:E.120 PG4.17: 5 residues within 4Å: Chain A: E.50, K.51, W.53, W.67, V.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.51 PG4.31: 5 residues within 4Å: Chain B: R.107, G.151, S.152, D.153, D.155 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.151, B:S.152, B:D.153, B:D.153 Water bridges: B:S.152 PG4.32: 5 residues within 4Å: Chain B: E.50, K.51, W.53, W.67 Ligands: EDO.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.51 PG4.33: 6 residues within 4Å: Chain A: E.188, K.211 Chain B: P.90, G.91, N.116, K.117 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.211, B:K.117 Water bridges: B:N.116 PG4.34: 9 residues within 4Å: Chain B: S.96, L.97, W.100, K.112, F.113, K.114, E.120, F.122, E.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.96, B:S.98, B:K.112, B:E.120 Water bridges: B:L.97

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

CL.18: 6 residues within 4Å: Chain A: G.101, N.102, G.103, A.104, G.105 Ligands: EDO.3 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain B: G.101, N.102, G.103, G.105 Ligands: EDO.20 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jia, N. et al., Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein. Embo Rep. (2016)

Release Date

2016-02-03

Peptides

Natterin-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Natterin-like protein

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