SMTL ID : 8a1d.1

Structure of murine perforin-2 (Mpeg1) pore in ring form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: Q.128, V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.3: 5 residues within 4Å: Chain B: Q.128, V.205, S.207, L.251, N.253 Ligand excluded by PLIP NAG.5: 6 residues within 4Å: Chain C: Q.128, V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.7: 6 residues within 4Å: Chain D: Q.128, V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain E: V.205, S.207, L.251, N.253 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain F: V.205, S.207, L.251, N.253 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain G: V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain H: V.205, S.207, L.251, N.253 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain I: V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain J: Q.128, V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain K: Q.128, V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain L: Q.128, V.205, S.207, L.251, N.253 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain M: V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain N: V.205, S.207, L.251, N.253 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain O: V.205, S.207, L.251, N.253, T.255 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain P: V.205, S.207, L.251, N.253 Ligand excluded by PLIP

16 x MA4: CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE(Non-covalent)

MA4.2: 7 residues within 4Å: Chain A: M.89, Y.250, G.410, Y.411, S.412, L.414, F.434 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.412, A:S.412, A:S.412, A:S.412 MA4.4: 7 residues within 4Å: Chain B: M.89, Y.250, G.410, Y.411, S.412, L.414, F.434 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.412, B:S.412, B:S.412 MA4.6: 7 residues within 4Å: Chain C: M.89, Y.250, G.410, Y.411, S.412, L.414, F.434 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.412, C:S.412, C:S.412 MA4.8: 7 residues within 4Å: Chain D: M.89, Y.250, G.410, Y.411, S.412, L.414, F.434 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.412, D:S.412, D:S.412 MA4.10: 6 residues within 4Å: Chain E: M.89, Y.250, G.410, Y.411, S.412, L.414 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.250, E:S.412 MA4.12: 5 residues within 4Å: Chain F: Y.250, G.410, Y.411, S.412, F.434 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.412, F:S.412, F:S.412, F:S.412 MA4.14: 7 residues within 4Å: Chain G: Y.250, E.409, G.410, Y.411, S.412, L.414, F.434 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:E.409, G:E.409, G:S.412, G:S.412 MA4.16: 8 residues within 4Å: Chain H: M.89, Y.250, E.409, G.410, Y.411, S.412, L.414, F.434 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:L.414 Hydrogen bonds: H:Y.250, H:E.409, H:E.409, H:S.412, H:S.412 MA4.18: 7 residues within 4Å: Chain I: M.89, Y.250, G.410, Y.411, S.412, L.414, F.434 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.412, I:S.412 MA4.20: 7 residues within 4Å: Chain J: M.89, Y.250, G.410, Y.411, S.412, L.414, F.434 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:S.412, J:S.412, J:S.412 MA4.22: 7 residues within 4Å: Chain K: M.89, Y.250, G.410, Y.411, S.412, L.414, F.434 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:S.412, K:S.412, K:S.412 MA4.24: 7 residues within 4Å: Chain L: M.89, Y.250, G.410, Y.411, S.412, L.414, F.434 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:S.412, L:S.412 MA4.26: 6 residues within 4Å: Chain M: M.89, Y.250, G.410, Y.411, S.412, L.414 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:Y.250, M:S.412, M:S.412 MA4.28: 6 residues within 4Å: Chain N: Y.250, G.410, Y.411, S.412, L.414, F.434 4 PLIP interactions: 4 interactions with chain N Hydrogen bonds: N:Y.250, N:S.412, N:S.412, N:S.412 MA4.30: 6 residues within 4Å: Chain O: Y.250, G.410, Y.411, S.412, L.414, F.434 5 PLIP interactions: 5 interactions with chain O Hydrogen bonds: O:Y.250, O:E.409, O:E.409, O:S.412, O:S.412 MA4.32: 9 residues within 4Å: Chain P: M.89, Y.250, E.409, G.410, Y.411, S.412, R.413, L.414, F.434 6 PLIP interactions: 6 interactions with chain P Hydrophobic interactions: P:R.413, P:L.414 Hydrogen bonds: P:E.409, P:E.409, P:S.412, P:S.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., Cryo-EM structures of perforin-2 in isolation and assembled on a membrane suggest a mechanism for pore formation. Embo J. (2022)

Release Date

2022-07-20

Peptides

Macrophage-expressed gene 1 protein: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Membrane

We predict this structure to be a membrane protein.
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Macrophage-expressed gene 1 protein

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