SMTL ID : 6u23.1

EM structure of MPEG-1(w.t.) soluble pre-pore

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

32 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: 4 residues within 4Å: Chain A: N.168, Q.587, T.590 Chain B: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.211 NAG-NAG.3: 4 residues within 4Å: Chain B: N.168, Q.587, T.590 Chain C: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.211 NAG-NAG.5: 4 residues within 4Å: Chain C: N.168, Q.587, T.590 Chain D: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain C: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.211 NAG-NAG.7: 4 residues within 4Å: Chain D: N.168, Q.587, T.590 Chain E: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain D: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.211 NAG-NAG.9: 4 residues within 4Å: Chain E: N.168, Q.587, T.590 Chain F: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain E: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.211 NAG-NAG.11: 4 residues within 4Å: Chain F: N.168, Q.587, T.590 Chain G: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain F: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.211 NAG-NAG.13: 4 residues within 4Å: Chain G: N.168, Q.587, T.590 Chain H: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain G: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.211 NAG-NAG.15: 4 residues within 4Å: Chain H: N.168, Q.587, T.590 Chain I: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain H: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.211 NAG-NAG.17: 4 residues within 4Å: Chain I: N.168, Q.587, T.590 Chain J: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain I: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.211 NAG-NAG.19: 4 residues within 4Å: Chain J: N.168, Q.587, T.590 Chain K: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain J: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:D.211 NAG-NAG.21: 4 residues within 4Å: Chain K: N.168, Q.587, T.590 Chain L: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain K: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.211 NAG-NAG.23: 3 residues within 4Å: Chain L: N.168, Q.587, T.590 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain L: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:D.211 NAG-NAG.25: 4 residues within 4Å: Chain M: N.168, Q.587, T.590 Chain N: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 6 residues within 4Å: Chain M: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:D.211 NAG-NAG.27: 4 residues within 4Å: Chain N: N.168, Q.587, T.590 Chain O: C.418 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 6 residues within 4Å: Chain N: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:D.211 NAG-NAG.29: 3 residues within 4Å: Chain O: N.168, Q.587, T.590 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 6 residues within 4Å: Chain O: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:D.211 NAG-NAG.31: 4 residues within 4Å: Chain A: C.418 Chain P: N.168, Q.587, T.590 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 6 residues within 4Å: Chain P: S.207, F.208, D.211, S.248, S.251, N.252 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:D.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, S.S. et al., The cryo-EM structure of the acid activatable pore-forming immune effector Macrophage-expressed gene 1. Nat Commun (2019)

Release Date

2019-09-25

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

Macrophage-expressed gene 1 protein