SMTL ID : 4xhs.1

Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 14 residues within 4Å: Chain A: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, W.341 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.63, A:R.67, A:R.67, A:E.154, A:Y.156 Water bridges: A:E.45, A:D.66 GLC-GLC.2: 17 residues within 4Å: Chain B: N.13, D.15, K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, M.331, W.341, R.345 Ligands: FMT.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.63, B:Y.156, B:R.345

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 2 residues within 4Å: Chain A: L.140, K.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.143 FMT.4: 5 residues within 4Å: Chain A: G.419, P.420, L.421, E.422 Chain B: R.371 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.419, A:L.421, A:E.422 FMT.7: 4 residues within 4Å: Chain B: N.119, L.122, K.145, G.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.119, B:K.145 Water bridges: B:D.121 FMT.8: 7 residues within 4Å: Chain B: E.45, E.46, R.67, Y.342, R.345 Ligands: GLC-GLC.2, NA.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.67, B:Y.342, B:R.345, B:R.345

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

NA.5: 2 residues within 4Å: Chain A: D.237, S.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.237 NA.6: 4 residues within 4Å: Chain A: R.67, S.338, W.341, Y.342 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.67, A:R.67, A:S.338, A:Y.342 Water bridges: A:E.46 NA.9: 3 residues within 4Å: Chain B: S.234, K.296, D.297 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.234, B:K.296 Water bridges: B:K.298 NA.10: 2 residues within 4Å: Chain B: Q.326, G.328 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.328 Water bridges: B:I.330 NA.11: 3 residues within 4Å: Chain B: D.237, S.239 Ligands: NA.12 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.237, B:S.239 NA.12: 2 residues within 4Å: Chain B: D.237 Ligands: NA.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.237 NA.13: 4 residues within 4Å: Chain B: S.338, W.341, Y.342 Ligands: FMT.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.342, B:Y.342, B:R.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, T. et al., Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction. To Be Published

Release Date

2016-01-27

Peptides

Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 12: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 12