SMTL ID : 6nla.1

Crystal structure of de novo designed metal-controlled dimer of B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: M.1, E.19, A.20 Ligands: CL.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.19 ZN.2: 4 residues within 4Å: Chain A: H.29, H.33 Chain B: H.12 Ligands: CL.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.29, A:H.33, B:H.12 ZN.9: 4 residues within 4Å: Chain B: M.1, E.19, A.20 Ligands: CL.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.19 ZN.10: 4 residues within 4Å: Chain A: H.12 Chain B: H.29, H.33 Ligands: CL.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.29, B:H.33, A:H.12

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

CL.3: 8 residues within 4Å: Chain A: I.18, H.29, H.33 Chain B: L.7, H.12, K.13, G.14 Ligands: ZN.2 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: M.1, E.19 Ligands: ZN.1 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: K.31 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain A: L.7, H.12, K.13, G.14 Chain B: I.18, H.29, H.33 Ligands: ZN.10 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: M.1, E.19 Ligands: ZN.9 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: K.31 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: I.18, E.19, A.20, H.29 Chain B: T.11, H.12, K.13 Ligands: NA.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:E.19 Hydrogen bonds: B:K.13, B:K.13 GOL.13: 8 residues within 4Å: Chain A: T.11, H.12, K.13 Chain B: I.18, E.19, A.20, H.29 Ligands: NA.15 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:E.19 Hydrogen bonds: A:K.13, A:K.13

4 x NA: SODIUM ION(Non-functional Binders)

NA.7: 2 residues within 4Å: Chain A: T.25 Ligands: GOL.5 No protein-ligand interaction detected (PLIP) NA.8: 2 residues within 4Å: Chain A: Y.45, D.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.47 NA.15: 2 residues within 4Å: Chain B: T.25 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.19 NA.16: 2 residues within 4Å: Chain B: Y.45, D.47 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maniaci, B. et al., Design of High-Affinity Metal-Controlled Protein Dimers. Biochemistry (2019)

Release Date

2019-01-23

Peptides

Immunoglobulin G-binding protein G: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Immunoglobulin G-binding protein G

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