SMTL ID : 4znr.1

Crystal structure of Dln1 complexed with Man(alpha1-3)Man

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 7 residues within 4Å: Chain A: G.34, G.35, R.107, G.151, S.152, D.153, D.155 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.35, A:G.151, A:S.152, A:D.153, A:D.153 Water bridges: A:G.34, A:D.155 MAN-MAN.2: 7 residues within 4Å: Chain B: G.34, G.35, R.107, G.151, S.152, D.153, D.155 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.35, B:G.151, B:S.152, B:D.153, B:D.153 Water bridges: B:G.34

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

CL.3: 5 residues within 4Å: Chain A: G.101, N.102, G.103, A.104, G.105 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: G.101, N.102, G.103, G.105 Ligand excluded by PLIP

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

PEG.4: 5 residues within 4Å: Chain A: Y.23, T.25, N.26, L.27, E.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.25, A:L.27 Water bridges: A:E.28 PEG.5: 7 residues within 4Å: Chain A: N.45, G.46, A.47, S.69, D.70, T.222, Y.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.222, A:Y.312 PEG.15: 4 residues within 4Å: Chain B: Y.23, T.25, N.26, L.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.26, B:L.27 PEG.16: 3 residues within 4Å: Chain B: W.128, G.129, K.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.129, B:K.131 PEG.17: 3 residues within 4Å: Chain B: V.201, K.202, E.204 No protein-ligand interaction detected (PLIP)

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

PGE.6: 8 residues within 4Å: Chain A: F.122, H.124, M.125, T.126, S.127, W.128, G.129, L.130 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.130, A:L.130 PGE.7: 6 residues within 4Å: Chain A: P.90, G.91, N.116, K.117 Chain B: E.188, K.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.90, A:N.116, A:K.117 PGE.18: 4 residues within 4Å: Chain B: E.50, K.51, W.67, V.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.51 Water bridges: B:R.65 PGE.19: 7 residues within 4Å: Chain B: H.124, M.125, T.126, S.127, W.128, G.129, L.130 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.130, B:L.130

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

PG4.8: 4 residues within 4Å: Chain A: E.50, K.51, W.67, V.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.51 PG4.9: 6 residues within 4Å: Chain A: W.100, K.112, K.114, E.120, F.122, E.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.112, A:K.112, A:K.114, A:K.114 PG4.20: 6 residues within 4Å: Chain B: W.100, K.112, K.114, E.120, F.122, E.133 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.112, B:K.114, B:K.114 Water bridges: B:S.98

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

EDO.10: 5 residues within 4Å: Chain A: I.29, S.37, V.147, G.148, R.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.149 EDO.13: 2 residues within 4Å: Chain B: K.327, N.329 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.327 EDO.14: 5 residues within 4Å: Chain B: S.37, F.38, V.147, G.148, R.149 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-covalent)

EPE.12: 5 residues within 4Å: Chain B: W.59, N.102, A.104, T.106, W.128 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.102, B:T.106 Water bridges: B:W.59, B:R.107 pi-Cation interactions: B:W.59, B:W.59

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.21: 6 residues within 4Å: Chain A: E.188, K.211 Chain B: P.90, G.91, N.116, K.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.117

Links

RCSB   PDBe   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

2016-01-20

Peptides

Natterin-like protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Natterin-like protein

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