SMTL ID : 3nsj.1

The X-ray crystal structure of lymphocyte perforin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Y.417, R.428, T.429, V.431, D.470 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.428, A:R.428, A:T.429 GOL.2: 7 residues within 4Å: Chain A: T.429, G.430, V.432, R.439, W.440, T.441, D.442 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.430, A:T.441, A:T.441, A:D.442 GOL.3: 4 residues within 4Å: Chain A: T.141, W.353, Q.354, L.521 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.353 Water bridges: A:R.361, A:R.361

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.465, Y.466, W.468, D.470 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.465, A:W.468, A:D.470, H2O.10 CA.5: 3 residues within 4Å: Chain A: D.415, D.463, A.464 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.415, A:D.463, A:A.464, H2O.6

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.6: 3 residues within 4Å: Chain A: L.176, N.333, K.335 Ligand excluded by PLIP IOD.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: V.381, R.389, Q.390, L.393 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: P.286, S.289, W.307 Ligand excluded by PLIP

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

CL.10: 3 residues within 4Å: Chain A: R.478, V.487, T.488 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: V.397, S.399, S.499, Y.500, H.501 Ligand excluded by PLIP

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

NAG.12: 4 residues within 4Å: Chain A: N.182, N.184, S.185, S.186 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.184 Hydrogen bonds: A:N.182, A:N.182, A:S.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Law, R.H. et al., The structural basis for membrane binding and pore formation by lymphocyte perforin. Nature (2010)

Release Date

2010-11-03

Peptides

Perforin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Perforin-1