SMTL ID : 4p99.1 (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

25 x CA: CALCIUM ION(Non-covalent)

CA.1: 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:D.333, A:D.420, H2O.5, H2O.12, H2O.14 CA.2: 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.4, H2O.4, H2O.5 CA.3: 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:T.243, A:D.245, A:V.247, A:E.252, H2O.4 CA.4: 4 residues within 4Å: Chain A: T.347, D.349, V.351, E.356 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.349, A:V.351, A:E.356, H2O.1, H2O.2 CA.5: 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.6, H2O.15 CA.6: 3 residues within 4Å: Chain A: D.350, T.433 Ligands: EDO.28 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.350, A:T.433, H2O.5, H2O.6, H2O.8 CA.7: 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.1, H2O.2, H2O.4, H2O.5 CA.8: 1 residues within 4Å: Chain A: D.101 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.101, A:D.101 CA.9: 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.5, H2O.6, 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.5, H2O.6, H2O.13, H2O.14 CA.11: 1 residues within 4Å: Chain A: T.78 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.78, H2O.1, H2O.1, H2O.3, H2O.3 CA.12: 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:T.35, A:D.37, A:V.39, A:E.44, H2O.4 CA.13: 2 residues within 4Å: Chain A: D.38, T.121 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.38, A:T.121, H2O.5, H2O.5, H2O.5 CA.14: 3 residues within 4Å: Chain A: D.97, A.99 Ligands: EDO.29 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.16 CA.15: 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.4, H2O.5 CA.16: 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.7, H2O.8 CA.17: 4 residues within 4Å: Chain A: T.139, D.141, V.143, E.148 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.143, A:E.148, A:E.148, H2O.7, H2O.7 CA.18: 2 residues within 4Å: Chain A: D.201, A.203 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.201, A:A.203, H2O.3, H2O.3, H2O.8 CA.19: 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.13, H2O.14 CA.20: 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.7, H2O.8, H2O.13, H2O.14 CA.21: 2 residues within 4Å: Chain A: E.23, D.108 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.23, A:D.108, H2O.1 CA.22: 2 residues within 4Å: Chain A: E.173, T.178 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.173, A:T.178 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.4 CA.24: 2 residues within 4Å: Chain A: D.309 Ligands: EDO.26 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.309, A:D.309, H2O.3 CA.33: 2 residues within 4Å: Chain A: E.69 Ligands: EDO.29 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.69, H2O.12

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

EDO.25: 2 residues within 4Å: Chain A: A.109, A.110 No protein-ligand interaction detected (PLIP) EDO.26: 3 residues within 4Å: Chain A: D.309, T.325 Ligands: CA.24 No protein-ligand interaction detected (PLIP) EDO.27: 3 residues within 4Å: Chain A: V.239, N.240, A.241 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.239, A:A.241, A:S.328 EDO.28: 3 residues within 4Å: Chain A: A.345, D.350 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Water bridges: A:V.343, A:N.344, A:D.350, A:S.432, A:T.433 EDO.29: 6 residues within 4Å: Chain A: E.69, N.71, G.72, D.97 Ligands: CA.14, CA.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.69, A:G.72 Water bridges: A:D.97, A:A.99 EDO.30: 2 residues within 4Å: Chain A: V.322, D.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.323 Water bridges: A:D.323, A:T.325 EDO.31: 5 residues within 4Å: Chain A: T.67, L.68, E.69, D.101, V.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.69, A:D.101, A:D.101 Water bridges: A:D.101 EDO.32: 3 residues within 4Å: Chain A: D.142, T.225, H.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.142 Water bridges: A:T.225, A:T.227 EDO.34: 1 residues within 4Å: Chain A: E.73 No protein-ligand interaction detected (PLIP) EDO.35: 2 residues within 4Å: Chain A: E.374, A.393 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.374

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
A

MpAFP_RII tetra-tandemer

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