SMTL ID : 5irb.3 (2 other biounits)

Structural insight into host cell surface retention of a 1.5-MDa bacterial ice-binding adhesin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

17 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: T.16, D.18, V.20, E.25 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.16, A:V.20, A:E.25, H2O.3, H2O.5 CA.2: 3 residues within 4Å: Chain A: D.209, S.211, D.296 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.211, A:D.296, H2O.1, H2O.3, H2O.7 CA.3: 2 residues within 4Å: Chain A: D.226, T.309 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.226, A:T.309, H2O.1, H2O.6, H2O.10 CA.4: 4 residues within 4Å: Chain A: T.120, D.122, V.124, E.129 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.120, A:D.122, A:V.124, H2O.1, H2O.1 CA.5: 2 residues within 4Å: Chain A: D.123, T.205 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.123, A:T.205, H2O.1, H2O.9, H2O.10 CA.6: 3 residues within 4Å: Chain A: D.77, D.79, I.81 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.79, A:I.81, H2O.2, H2O.5, H2O.9 CA.7: 1 residues within 4Å: Chain A: Q.191 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:Q.191, H2O.1, H2O.2, H2O.10, H2O.10 CA.8: 2 residues within 4Å: Chain A: D.181, S.183 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.181, H2O.3, H2O.7, H2O.7, H2O.8 CA.9: 4 residues within 4Å: Chain A: T.223, D.225, V.227, E.232 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.223, A:D.225, A:V.227, H2O.4, H2O.5 CA.10: 4 residues within 4Å: Chain A: D.285, A.287 Chain B: D.285, A.287 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.285, B:A.287, A:D.285, A:A.287, H2O.12 CA.11: 4 residues within 4Å: Chain B: T.16, D.18, V.20, E.25 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.16, B:V.20, B:E.25, H2O.12, H2O.17 CA.12: 3 residues within 4Å: Chain B: D.77, D.79, I.81 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.77, B:I.81, H2O.12, H2O.13, H2O.16 CA.13: 3 residues within 4Å: Chain B: D.209, S.211, D.296 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.209, B:S.211, B:D.296, H2O.14, H2O.19 CA.14: 4 residues within 4Å: Chain B: T.120, D.122, V.124, E.129 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.120, B:D.122, B:V.124, H2O.13, H2O.16 CA.15: 2 residues within 4Å: Chain B: D.226, T.309 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.226, B:T.309, H2O.14, H2O.20, H2O.21 CA.16: 2 residues within 4Å: Chain B: D.123, T.205 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.123, B:T.205, H2O.12, H2O.20, H2O.21 CA.17: 4 residues within 4Å: Chain B: T.223, D.225, V.227, E.232 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.223, B:D.225, B:V.227, H2O.12, H2O.13

2 x MG: MAGNESIUM ION(Non-covalent)

MG.18: 2 residues within 4Å: Chain B: D.181, S.183 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.181, B:S.183, H2O.12, H2O.14, H2O.15, H2O.16 MG.19: 3 residues within 4Å: Chain B: I.12, E.102 Ligands: EDO.20 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:I.12, B:E.102, H2O.14, H2O.15, H2O.16

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.20: 5 residues within 4Å: Chain B: D.11, I.12, D.13, P.14 Ligands: MG.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, S. et al., Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice. Sci Adv (2017)

Release Date

2017-07-19

Peptides

RTX-adhesin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RTX-adhesin

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