SMTL ID : 1g9u.1

CRYSTAL STRUCTURE OF YOPM-LEUCINE RICH EFFECTOR PROTEIN FROM YERSINIA PESTIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

36 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: R.383, M.384, N.385 Chain D: D.381, L.382, R.383 Ligand excluded by PLIP ACT.2: 6 residues within 4Å: Chain A: D.203, V.221, G.223, Y.243, D.245 Ligands: ACT.6 Ligand excluded by PLIP ACT.3: 5 residues within 4Å: Chain A: T.251, L.252, D.271, L.272, P.273 Ligand excluded by PLIP ACT.4: 4 residues within 4Å: Chain A: W.46, N.49, R.58, S.85 Ligand excluded by PLIP ACT.5: 7 residues within 4Å: Chain A: D.128, L.129, P.147, E.148, L.149, N.151, S.152 Ligand excluded by PLIP ACT.6: 6 residues within 4Å: Chain A: D.245, N.246, N.263, R.265 Ligands: ACT.2, ACT.9 Ligand excluded by PLIP ACT.7: 4 residues within 4Å: Chain A: P.257, P.276, Q.277, S.278 Ligand excluded by PLIP ACT.8: 8 residues within 4Å: Chain A: L.292, S.293, E.294, L.295, L.312, C.313, D.314, L.315 Ligand excluded by PLIP ACT.9: 1 residues within 4Å: Ligands: ACT.6 Ligand excluded by PLIP ACT.20: 6 residues within 4Å: Chain B: R.383, M.384, N.385 Chain C: D.381, L.382, R.383 Ligand excluded by PLIP ACT.21: 6 residues within 4Å: Chain B: D.203, V.221, G.223, Y.243, D.245 Ligands: ACT.25 Ligand excluded by PLIP ACT.22: 5 residues within 4Å: Chain B: T.251, L.252, D.271, L.272, P.273 Ligand excluded by PLIP ACT.23: 4 residues within 4Å: Chain B: W.46, N.49, R.58, S.85 Ligand excluded by PLIP ACT.24: 7 residues within 4Å: Chain B: D.128, L.129, P.147, E.148, L.149, N.151, S.152 Ligand excluded by PLIP ACT.25: 6 residues within 4Å: Chain B: D.245, N.246, N.263, R.265 Ligands: ACT.21, ACT.28 Ligand excluded by PLIP ACT.26: 4 residues within 4Å: Chain B: P.257, P.276, Q.277, S.278 Ligand excluded by PLIP ACT.27: 8 residues within 4Å: Chain B: L.292, S.293, E.294, L.295, L.312, C.313, D.314, L.315 Ligand excluded by PLIP ACT.28: 1 residues within 4Å: Ligands: ACT.25 Ligand excluded by PLIP ACT.39: 6 residues within 4Å: Chain B: D.381, L.382, R.383 Chain C: R.383, M.384, N.385 Ligand excluded by PLIP ACT.40: 6 residues within 4Å: Chain C: D.203, V.221, G.223, Y.243, D.245 Ligands: ACT.44 Ligand excluded by PLIP ACT.41: 5 residues within 4Å: Chain C: T.251, L.252, D.271, L.272, P.273 Ligand excluded by PLIP ACT.42: 4 residues within 4Å: Chain C: W.46, N.49, R.58, S.85 Ligand excluded by PLIP ACT.43: 7 residues within 4Å: Chain C: D.128, L.129, P.147, E.148, L.149, N.151, S.152 Ligand excluded by PLIP ACT.44: 6 residues within 4Å: Chain C: D.245, N.246, N.263, R.265 Ligands: ACT.40, ACT.47 Ligand excluded by PLIP ACT.45: 4 residues within 4Å: Chain C: P.257, P.276, Q.277, S.278 Ligand excluded by PLIP ACT.46: 8 residues within 4Å: Chain C: L.292, S.293, E.294, L.295, L.312, C.313, D.314, L.315 Ligand excluded by PLIP ACT.47: 1 residues within 4Å: Ligands: ACT.44 Ligand excluded by PLIP ACT.58: 6 residues within 4Å: Chain A: D.381, L.382, R.383 Chain D: R.383, M.384, N.385 Ligand excluded by PLIP ACT.59: 6 residues within 4Å: Chain D: D.203, V.221, G.223, Y.243, D.245 Ligands: ACT.63 Ligand excluded by PLIP ACT.60: 5 residues within 4Å: Chain D: T.251, L.252, D.271, L.272, P.273 Ligand excluded by PLIP ACT.61: 4 residues within 4Å: Chain D: W.46, N.49, R.58, S.85 Ligand excluded by PLIP ACT.62: 7 residues within 4Å: Chain D: D.128, L.129, P.147, E.148, L.149, N.151, S.152 Ligand excluded by PLIP ACT.63: 6 residues within 4Å: Chain D: D.245, N.246, N.263, R.265 Ligands: ACT.59, ACT.66 Ligand excluded by PLIP ACT.64: 4 residues within 4Å: Chain D: P.257, P.276, Q.277, S.278 Ligand excluded by PLIP ACT.65: 8 residues within 4Å: Chain D: L.292, S.293, E.294, L.295, L.312, C.313, D.314, L.315 Ligand excluded by PLIP ACT.66: 1 residues within 4Å: Ligands: ACT.63 Ligand excluded by PLIP

8 x CA: CALCIUM ION(Non-covalent)

CA.10: 3 residues within 4Å: Chain A: N.246, D.266 Chain B: N.326 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.266, H2O.5, H2O.5, H2O.7 CA.11: 3 residues within 4Å: Chain A: D.266 Chain B: N.307, E.308 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.308, A:D.266, H2O.5, H2O.5, H2O.5 CA.29: 3 residues within 4Å: Chain A: N.326 Chain B: N.246, D.266 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.266, H2O.14, H2O.14, H2O.16 CA.30: 3 residues within 4Å: Chain A: N.307, E.308 Chain B: D.266 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.308, B:D.266, H2O.14, H2O.14, H2O.14 CA.48: 3 residues within 4Å: Chain C: N.246, D.266 Chain D: N.326 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.266, H2O.23, H2O.23, H2O.25 CA.49: 3 residues within 4Å: Chain C: D.266 Chain D: N.307, E.308 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:D.266, D:E.308, H2O.23, H2O.23, H2O.23 CA.67: 3 residues within 4Å: Chain C: N.326 Chain D: N.246, D.266 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.266, H2O.32, H2O.32, H2O.34 CA.68: 3 residues within 4Å: Chain C: N.307, E.308 Chain D: D.266 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:E.308, D:D.266, H2O.32, H2O.32, H2O.32

32 x HG: MERCURY (II) ION(Non-covalent)(Non-functional Binders)

HG.12: 4 residues within 4Å: Chain A: C.68, Q.72, A.73, P.90 Ligand excluded by PLIP HG.13: 3 residues within 4Å: Chain A: Q.72, P.91, H.92 Ligand excluded by PLIP HG.14: 3 residues within 4Å: Chain A: I.330, H.348 Chain B: S.206 Ligand excluded by PLIP HG.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HG.16: 3 residues within 4Å: Chain A: I.343, H.363, E.365 Ligand excluded by PLIP HG.17: 4 residues within 4Å: Chain A: N.347, H.348, P.368 Chain B: N.224 Ligand excluded by PLIP HG.18: 2 residues within 4Å: Chain A: N.80, C.100 Ligand excluded by PLIP HG.19: 1 residues within 4Å: Chain A: C.100 Ligand excluded by PLIP HG.31: 4 residues within 4Å: Chain B: C.68, Q.72, A.73, P.90 Ligand excluded by PLIP HG.32: 3 residues within 4Å: Chain B: Q.72, P.91, H.92 Ligand excluded by PLIP HG.33: 3 residues within 4Å: Chain A: S.206 Chain B: I.330, H.348 Ligand excluded by PLIP HG.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HG.35: 3 residues within 4Å: Chain B: I.343, H.363, E.365 Ligand excluded by PLIP HG.36: 4 residues within 4Å: Chain A: N.224 Chain B: N.347, H.348, P.368 Ligand excluded by PLIP HG.37: 2 residues within 4Å: Chain B: N.80, C.100 Ligand excluded by PLIP HG.38: 1 residues within 4Å: Chain B: C.100 Ligand excluded by PLIP HG.50: 4 residues within 4Å: Chain C: C.68, Q.72, A.73, P.90 Ligand excluded by PLIP HG.51: 3 residues within 4Å: Chain C: Q.72, P.91, H.92 Ligand excluded by PLIP HG.52: 3 residues within 4Å: Chain C: I.330, H.348 Chain D: S.206 Ligand excluded by PLIP HG.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HG.54: 3 residues within 4Å: Chain C: I.343, H.363, E.365 Ligand excluded by PLIP HG.55: 4 residues within 4Å: Chain C: N.347, H.348, P.368 Chain D: N.224 Ligand excluded by PLIP HG.56: 2 residues within 4Å: Chain C: N.80, C.100 Ligand excluded by PLIP HG.57: 1 residues within 4Å: Chain C: C.100 Ligand excluded by PLIP HG.69: 4 residues within 4Å: Chain D: C.68, Q.72, A.73, P.90 Ligand excluded by PLIP HG.70: 3 residues within 4Å: Chain D: Q.72, P.91, H.92 Ligand excluded by PLIP HG.71: 3 residues within 4Å: Chain C: S.206 Chain D: I.330, H.348 Ligand excluded by PLIP HG.72: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HG.73: 3 residues within 4Å: Chain D: I.343, H.363, E.365 Ligand excluded by PLIP HG.74: 4 residues within 4Å: Chain C: N.224 Chain D: N.347, H.348, P.368 Ligand excluded by PLIP HG.75: 2 residues within 4Å: Chain D: N.80, C.100 Ligand excluded by PLIP HG.76: 1 residues within 4Å: Chain D: C.100 Ligand excluded by 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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