SMTL ID : 4xgo.1

Crystal structure of leucine-rich repeat domain of APL1B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: S.127, S.128, N.146, S.148, Y.149, E.163, D.165 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.149 NAG-NAG.2: 6 residues within 4Å: Chain B: S.127, N.146, S.148, Y.149, E.163, D.165 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.149

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: T.193, D.194, T.195, L.214, K.216, I.217, T.218, H.221 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.195, A:A.196, A:K.216, A:K.216, A:T.218 Water bridges: A:E.215 Salt bridges: A:H.221 PO4.13: 3 residues within 4Å: Chain B: T.132, H.133, T.154 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.154 Water bridges: B:R.109, B:R.109, B:T.154 Salt bridges: B:H.133 PO4.14: 3 residues within 4Å: Chain B: Q.188, H.189, Y.211 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.188 Salt bridges: B:H.189

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: R.55, F.56, D.79, R.80, S.103, N.104 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.79, A:R.80 Hydrogen bonds: A:N.104 Salt bridges: A:R.55, A:R.80 ACT.12: 6 residues within 4Å: Chain B: D.194, T.195, K.216, I.217, T.218, H.221 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.194 Hydrogen bonds: B:T.195, B:T.218 Salt bridges: B:H.221

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: H.302, N.303, D.326, H.328, C.329, K.330, C.340 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.302, A:N.303, A:N.303, A:D.326, A:K.330 Water bridges: A:H.302 GOL.6: 5 residues within 4Å: Chain A: H.168, Q.188, H.189, S.210, Y.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.188, A:H.189, A:S.210 Water bridges: A:D.208, A:D.208 GOL.7: 4 residues within 4Å: Chain A: Y.5, Q.125, N.146 Ligands: NAG-NAG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.5, A:Y.5, A:Q.125, A:N.146 GOL.8: 2 residues within 4Å: Chain A: N.191, Q.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.191, A:Q.213 Water bridges: A:T.170, A:T.170, A:N.172 GOL.9: 4 residues within 4Å: Chain A: R.109, T.132, H.133, T.154 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.109, A:T.154 Water bridges: A:T.132, A:T.132, A:T.132, A:S.153, A:S.153, A:T.154 GOL.10: 3 residues within 4Å: Chain A: H.189, N.190, Y.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.189, A:N.190 Water bridges: A:H.168, A:H.168

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

CL.11: 3 residues within 4Å: Chain A: G.89, H.92, D.113 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: N.123, H.144 Ligand excluded by PLIP

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

NA.16: 8 residues within 4Å: Chain B: N.179, V.180, E.181, L.182, Y.201, P.202, G.203, L.204 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.179, B:G.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, M. et al., Biophysical Analysis of Anopheles gambiae Leucine-Rich Repeat Proteins APL1A1, APLB and APL1C and Their Interaction with LRIM1. Plos One (2015)

Release Date

2015-04-01

Peptides

Anopheles Plasmodium-responsive Leucine-rich repeat protein 1B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Anopheles Plasmodium-responsive Leucine-rich repeat protein 1B