SMTL ID : 3sb5.2 (3 other biounits)

Zn-mediated Trimer of T4 Lysozyme R125C/E128C by Synthetic Symmetrization

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-trimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 9 residues within 4Å: Chain A: C.128, C.131 Chain B: C.128 Ligands: ZN.2, CL.4, ZN.10, ZN.11, ZN.19, ZN.20 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:C.128, A:C.131, B:C.128 ZN.2: 11 residues within 4Å: Chain A: C.131 Chain B: C.131 Chain C: C.131 Ligands: ZN.1, CL.7, ZN.10, ZN.11, CL.16, ZN.19, ZN.20, CL.25 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:C.131, A:C.131, C:C.131 ZN.10: 9 residues within 4Å: Chain B: C.128, C.131 Chain C: C.128 Ligands: ZN.1, ZN.2, ZN.11, CL.13, ZN.19, ZN.20 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Metal complexes: B:C.128, B:C.131, C:C.128 ZN.11: 11 residues within 4Å: Chain A: C.131 Chain B: C.131 Chain C: C.131 Ligands: ZN.1, ZN.2, CL.7, ZN.10, CL.16, ZN.19, ZN.20, CL.25 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:C.131, A:C.131, C:C.131 ZN.19: 9 residues within 4Å: Chain A: C.128 Chain C: C.128, C.131 Ligands: ZN.1, ZN.2, ZN.10, ZN.11, ZN.20, CL.22 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:C.128, C:C.131, A:C.128 ZN.20: 11 residues within 4Å: Chain A: C.131 Chain B: C.131 Chain C: C.131 Ligands: ZN.1, ZN.2, CL.7, ZN.10, ZN.11, CL.16, ZN.19, CL.25 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:C.131, A:C.131, B:C.131

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: E.14, I.32, G.33, D.73, F.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.73, A:D.73 GOL.6: 6 residues within 4Å: Chain A: S.93, L.94, L.124, Q.125, K.127, W.129 No protein-ligand interaction detected (PLIP) GOL.8: 4 residues within 4Å: Chain A: I.6, A.96, R.99, I.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.96 Water bridges: A:Y.91, A:R.99 GOL.12: 5 residues within 4Å: Chain B: E.14, I.32, G.33, D.73, F.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.73, B:D.73 GOL.15: 6 residues within 4Å: Chain B: S.93, L.94, L.124, Q.125, K.127, W.129 No protein-ligand interaction detected (PLIP) GOL.17: 4 residues within 4Å: Chain B: I.6, A.96, R.99, I.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.96 Water bridges: B:Y.91, B:R.99 GOL.21: 5 residues within 4Å: Chain C: E.14, I.32, G.33, D.73, F.107 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.73, C:D.73 GOL.24: 6 residues within 4Å: Chain C: S.93, L.94, L.124, Q.125, K.127, W.129 No protein-ligand interaction detected (PLIP) GOL.26: 4 residues within 4Å: Chain C: I.6, A.96, R.99, I.103 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.96 Water bridges: C:Y.91, C:R.99

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

CL.4: 6 residues within 4Å: Chain A: C.128, D.130, C.131 Chain B: Q.126, C.128 Ligands: ZN.1 Ligand excluded by PLIP CL.7: 8 residues within 4Å: Chain A: C.131 Chain B: C.131 Chain C: C.131 Ligands: ZN.2, ZN.11, CL.16, ZN.20, CL.25 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: C.128, D.130, C.131 Chain C: Q.126, C.128 Ligands: ZN.10 Ligand excluded by PLIP CL.16: 8 residues within 4Å: Chain A: C.131 Chain B: C.131 Chain C: C.131 Ligands: ZN.2, CL.7, ZN.11, ZN.20, CL.25 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain A: Q.126, C.128 Chain C: C.128, D.130, C.131 Ligands: ZN.19 Ligand excluded by PLIP CL.25: 8 residues within 4Å: Chain A: C.131 Chain B: C.131 Chain C: C.131 Ligands: ZN.2, CL.7, ZN.11, CL.16, ZN.20 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: T.145, P.146, N.147, R.148 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: F.117, N.119, S.120, N.135 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.120 MG.14: 4 residues within 4Å: Chain B: T.145, P.146, N.147, R.148 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain B: F.117, N.119, S.120, N.135 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.120 MG.23: 4 residues within 4Å: Chain C: T.145, P.146, N.147, R.148 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain C: F.117, N.119, S.120, N.135 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laganowsky, A. et al., An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Protein Sci. (2011)

Release Date

2011-09-21

Peptides

Lysozyme: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Lysozyme

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