SMTL ID : 1jl5.1

Novel Molecular Architecture of YopM-a Leucine-rich Effector Protein from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: N.246, D.266, E.286 Chain C: N.326 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.266, H2O.1, H2O.1, H2O.2 CA.2: 3 residues within 4Å: Chain A: D.266 Chain C: N.307, E.308 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:E.308, A:D.266, H2O.1, H2O.1, H2O.1 CA.3: 2 residues within 4Å: Chain A: N.162, N.182 No protein-ligand interaction detected (PLIP) CA.4: 2 residues within 4Å: Chain A: E.274, E.294 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.274, A:E.294, A:E.294, H2O.9, H2O.13 CA.5: 1 residues within 4Å: Chain A: E.59 No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain B: N.246, D.266, E.286 Chain D: N.326 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.266, H2O.14, H2O.14, H2O.15 CA.7: 3 residues within 4Å: Chain B: D.266 Chain D: N.307, E.308 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: B:D.266, D:E.308, H2O.14, H2O.14, H2O.14 CA.8: 2 residues within 4Å: Chain B: N.162, N.182 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain B: E.274, E.294 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.274, B:E.294, B:E.294, H2O.22, H2O.26 CA.10: 1 residues within 4Å: Chain B: E.59 No protein-ligand interaction detected (PLIP) CA.11: 4 residues within 4Å: Chain A: N.326 Chain C: N.246, D.266, E.286 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.266, H2O.27, H2O.27, H2O.28 CA.12: 3 residues within 4Å: Chain A: N.307, E.308 Chain C: D.266 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.266, A:E.308, H2O.27, H2O.27, H2O.27 CA.13: 2 residues within 4Å: Chain C: N.162, N.182 No protein-ligand interaction detected (PLIP) CA.14: 2 residues within 4Å: Chain C: E.274, E.294 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.274, C:E.294, C:E.294, H2O.35, H2O.39 CA.15: 1 residues within 4Å: Chain C: E.59 No protein-ligand interaction detected (PLIP) CA.16: 4 residues within 4Å: Chain B: N.326 Chain D: N.246, D.266, E.286 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.266, H2O.40, H2O.40, H2O.41 CA.17: 3 residues within 4Å: Chain B: N.307, E.308 Chain D: D.266 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: B:E.308, D:D.266, H2O.40, H2O.40, H2O.40 CA.18: 2 residues within 4Å: Chain D: N.162, N.182 No protein-ligand interaction detected (PLIP) CA.19: 2 residues within 4Å: Chain D: E.274, E.294 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.274, D:E.294, D:E.294, H2O.48, H2O.52 CA.20: 1 residues within 4Å: Chain D: E.59 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evdokimov, A.G. et al., Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit. J.Mol.Biol. (2001)

Release Date

2001-10-10

Peptides

outer protein YopM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

outer protein YopM

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