SMTL ID : 4p99.3 (3 other biounits)

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

30 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: D.101 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.101, A:D.101, H2O.10 CA.2: 1 residues within 4Å: Chain A: D.205 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.205, A:D.205 CA.4: 3 residues within 4Å: Chain A: D.333, E.335, D.420 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.335, A:D.420, H2O.13, H2O.13, H2O.13 CA.5: 2 residues within 4Å: Chain A: D.201, A.203 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.201, A:D.201, A:A.203, H2O.5, H2O.16 CA.6: 2 residues within 4Å: Chain A: E.23, D.108 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.23, A:D.108, H2O.1, H2O.4 CA.7: 2 residues within 4Å: Chain A: D.38, T.121 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.121, H2O.6, H2O.6, H2O.6, H2O.16 CA.8: 4 residues within 4Å: Chain A: T.35, D.37, V.39, E.44 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.37, A:V.39, A:E.44, A:E.44, H2O.6 CA.9: 3 residues within 4Å: Chain A: D.125, E.127, D.212 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:E.127, A:D.212, H2O.6, H2O.6 CA.10: 1 residues within 4Å: Chain A: S.107 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.107, H2O.4, H2O.6, H2O.6, H2O.19 CA.11: 4 residues within 4Å: Chain A: T.139, D.141, V.143, E.148 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.141, A:V.143, A:E.148, A:E.148, H2O.12 CA.12: 2 residues within 4Å: Chain A: D.142, T.225 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.142, A:T.225, H2O.7, H2O.13, H2O.15 CA.13: 3 residues within 4Å: Chain A: D.229, E.231, D.316 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.229, A:E.231, A:D.316, H2O.7, H2O.7 CA.14: 2 residues within 4Å: Chain A: D.246, T.329 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.246, A:T.329, H2O.7, H2O.7, H2O.7 CA.15: 4 residues within 4Å: Chain A: T.243, D.245, V.247, E.252 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.245, A:V.247, A:E.252, A:E.252, H2O.7 CA.16: 2 residues within 4Å: Chain A: D.97, A.99 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:D.97, A:A.99, H2O.6, H2O.6 CA.17: 1 residues within 4Å: Chain A: S.211 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.211, H2O.4, H2O.7, H2O.12, H2O.15 CA.18: 2 residues within 4Å: Chain A: E.73 Ligands: BOG.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.73, H2O.5, H2O.8, H2O.13 CA.19: 3 residues within 4Å: Chain A: E.177 Ligands: EDO.32, TRS.41 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.177, H2O.2, H2O.8, H2O.8 CA.20: 2 residues within 4Å: Chain A: A.81, N.82 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.81, H2O.2 CA.21: 1 residues within 4Å: Chain A: S.315 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.315, H2O.9, H2O.12, H2O.12, H2O.12 CA.22: 2 residues within 4Å: Chain A: A.185, N.186 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.185, H2O.3 CA.23: 2 residues within 4Å: Chain A: D.305, A.307 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.305, A:D.305, A:A.307, H2O.1, H2O.3 CA.24: 1 residues within 4Å: Chain A: E.281 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.281, H2O.2, H2O.4, H2O.12 CA.25: 2 residues within 4Å: Chain A: D.350, T.433 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.350, A:T.433, H2O.14, H2O.14, H2O.15 CA.26: 4 residues within 4Å: Chain A: T.347, D.349, V.351, E.356 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.347, A:D.349, A:E.356, A:E.356, H2O.1 CA.27: 1 residues within 4Å: Chain A: S.419 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.419, H2O.14, H2O.14, H2O.14, H2O.14 CA.28: 2 residues within 4Å: Chain A: D.409, A.411 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.409, A:D.409, A:A.411, H2O.1, H2O.4 CA.29: 2 residues within 4Å: Chain A: E.385 Ligands: BOG.42 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.385, H2O.2, H2O.4, H2O.14, H2O.16 CA.30: 1 residues within 4Å: Chain A: G.370 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.370, H2O.17 CA.31: 1 residues within 4Å: Chain A: G.162 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.162, H2O.9

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 3 residues within 4Å: Chain A: G.72, E.73 Ligands: CA.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.73 BOG.42: 3 residues within 4Å: Chain A: G.384, E.385 Ligands: CA.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.385, A:E.385, A:E.385

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

EDO.32: 4 residues within 4Å: Chain A: G.176, E.177 Ligands: CA.19, TRS.41 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.177 EDO.33: 3 residues within 4Å: Chain A: T.35, V.49, A.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.36, A:A.50 Water bridges: A:T.35 EDO.34: 3 residues within 4Å: Chain A: E.177, T.178, Y.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.179 EDO.35: 7 residues within 4Å: Chain A: T.160, E.166, V.183, D.184, A.185, N.186, G.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.160, A:E.166, A:D.184, A:G.187 EDO.36: 4 residues within 4Å: Chain A: E.127, A.128, T.129, A.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.130 EDO.37: 4 residues within 4Å: Chain A: A.42, A.45, A.46, T.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.126 EDO.38: 2 residues within 4Å: Chain A: N.344, A.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.345 EDO.39: 5 residues within 4Å: Chain A: T.379, L.380, E.381, D.413, V.415 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.381, A:E.381, A:D.413, A:D.413 EDO.40: 2 residues within 4Å: Chain A: N.136, A.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.137

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.41: 3 residues within 4Å: Chain A: E.177 Ligands: CA.19, EDO.32 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vance, T.D. et al., Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice. Biosci.Rep. (2014)

Release Date

2014-06-18

Peptides

MpAFP_RII tetra-tandemer: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

MpAFP_RII tetra-tandemer

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