SMTL ID : 2g2p.1

Crystal Structure of E.coli transthyretin-related protein with bound Zn and Br

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

15 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.9, H.98 Ligands: BR.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.9, A:H.98, H2O.1 ZN.2: 3 residues within 4Å: Chain A: H.96, H.98, S.114 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.98, A:S.114, H2O.2 ZN.3: 2 residues within 4Å: Chain A: H.96, S.114 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:S.114, A:S.114 ZN.4: 3 residues within 4Å: Chain A: G.60, D.61, H.89 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.61, A:H.89, H2O.2 ZN.8: 3 residues within 4Å: Chain B: H.9, H.98 Ligands: BR.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.9, B:H.98, H2O.3 ZN.9: 4 residues within 4Å: Chain B: H.96, H.98, S.114 Ligands: ZN.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.96, B:H.98, B:S.114, H2O.4 ZN.10: 3 residues within 4Å: Chain B: H.96, S.114 Ligands: ZN.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:S.114, B:S.114 ZN.11: 2 residues within 4Å: Chain B: D.61, H.89 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.61, B:H.89, H2O.4 ZN.14: 3 residues within 4Å: Chain C: H.9, H.98 Ligands: BR.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.9, C:H.98, H2O.4 ZN.15: 3 residues within 4Å: Chain C: H.96, H.98, S.114 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.96, C:H.98, C:S.114 ZN.16: 2 residues within 4Å: Chain C: D.61, H.89 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.61, C:H.89, H2O.5 ZN.19: 3 residues within 4Å: Chain D: H.9, H.98 Ligands: BR.23 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.9, D:H.98, H2O.6 ZN.20: 4 residues within 4Å: Chain D: H.96, H.98, S.114 Ligands: ZN.21 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.96, D:H.98, D:S.114 ZN.21: 4 residues within 4Å: Chain D: Q.3, H.96, S.114 Ligands: ZN.20 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.96, D:S.114 ZN.22: 2 residues within 4Å: Chain D: D.61, H.89 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.61, D:H.89, H2O.6

4 x BR: BROMIDE ION(Non-covalent)

BR.5: 6 residues within 4Å: Chain A: S.7, V.8, H.9, R.47, H.98 Ligands: ZN.1 Ligand excluded by PLIP BR.12: 6 residues within 4Å: Chain B: S.7, V.8, H.9, R.47, H.98 Ligands: ZN.8 Ligand excluded by PLIP BR.17: 8 residues within 4Å: Chain C: S.7, V.8, H.9, R.47, I.48, K.49, H.98 Ligands: ZN.14 Ligand excluded by PLIP BR.23: 6 residues within 4Å: Chain D: S.7, V.8, H.9, R.47, H.98 Ligands: ZN.19 Ligand excluded by PLIP

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: W.34, R.63 Chain B: W.34, R.63 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.34 Water bridges: B:R.63 Salt bridges: B:R.63, A:R.63 SO4.7: 8 residues within 4Å: Chain A: H.9, H.98, P.100, Y.111, G.113, S.114 Chain C: H.9, Y.111 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.114, C:Y.111 Salt bridges: A:H.9, A:H.98, C:H.9 SO4.13: 9 residues within 4Å: Chain B: H.9, H.98, P.100, Y.111, G.113, S.114 Chain D: H.9, L.11 Ligands: SO4.24 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain B Water bridges: D:H.9 Salt bridges: D:H.9, B:H.9, B:H.98 Hydrogen bonds: B:Y.111, B:Y.111, B:S.114, B:S.114 SO4.18: 4 residues within 4Å: Chain C: W.34, R.63 Chain D: W.34, R.63 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Water bridges: C:W.34, C:W.34, C:R.63, D:R.63 Salt bridges: C:R.63, D:R.63 SO4.24: 7 residues within 4Å: Chain B: H.9 Chain D: H.98, P.100, Y.111, G.113, S.114 Ligands: SO4.13 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.114, D:S.114 Salt bridges: D:H.9, D:H.98, B:H.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lundberg, E. et al., The transthyretin-related protein: structural investigation of a novel protein family. J.Struct.Biol. (2006)

Release Date

2006-12-12

Peptides

Transthyretin-like protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Transthyretin-like protein

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