SMTL ID : 6x5w.1

Peptide-bound structure of Marinomonas primoryensis peptide-binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x GLY- TYR- THR- ASP: peptide(Non-covalent)

GLY-TYR-THR-ASP.1: 15 residues within 4Å: Chain A: A.254, Y.290, P.291, V.292, Y.293, S.294, G.295, E.329, T.330, P.331, N.332, D.341, E.384 Ligands: CA.3, CA.16 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.254, A:E.329 Hydrogen bonds: A:V.292, A:V.292, A:S.294, A:S.294, A:G.295, A:E.329, A:T.330, A:T.330, A:N.332, A:N.332

18 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 3 residues within 4Å: Chain A: S.427, T.429, Q.490 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.427, H2O.2 CA.3: 8 residues within 4Å: Chain A: N.289, T.330, N.332, S.339, D.341, E.384 Ligands: GLY-TYR-THR-ASP.1, CA.16 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.330, A:T.330, A:S.339, A:D.341, A:E.384 CA.4: 8 residues within 4Å: Chain A: D.190, S.191, A.192, D.425, D.489, D.491, S.493 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.191, A:D.425, A:D.489, A:D.491, A:S.493 CA.5: 8 residues within 4Å: Chain A: E.115, R.160, H.162, D.190, S.191, D.425, D.491 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.115, A:R.160, A:D.190, A:D.425, A:D.491 CA.6: 5 residues within 4Å: Chain A: D.161, H.162, D.164, V.166, D.168 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.161, A:D.164, A:V.166, H2O.6, H2O.8 CA.7: 7 residues within 4Å: Chain A: E.213, I.214, A.215, N.241, D.242, D.265, D.267 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.214, A:D.242, A:D.265, A:D.267, H2O.15 CA.8: 5 residues within 4Å: Chain A: V.196, D.198, I.411, D.420, Y.485 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.196, A:D.198, A:I.411, A:D.420, A:Y.485 CA.9: 5 residues within 4Å: Chain A: T.13, D.15, T.17, I.18, E.22 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.13, A:E.22, A:E.22, H2O.4, H2O.16 CA.10: 4 residues within 4Å: Chain A: D.231, D.240, D.242, S.243 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.231, A:D.240, A:D.240, H2O.5, H2O.18 CA.11: 6 residues within 4Å: Chain A: A.11, I.12, D.16, S.99, T.100, H.101 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.16, A:T.100, H2O.5, H2O.6, H2O.18 CA.12: 1 residues within 4Å: Chain A: G.24 No protein-ligand interaction detected (PLIP) CA.13: 6 residues within 4Å: Chain A: D.231, G.232, D.240, D.242, A.244, D.246 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.240, A:D.242, A:A.244, A:D.246, H2O.8 CA.14: 3 residues within 4Å: Chain A: D.76, E.78, F.79 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.76, A:E.78, H2O.7, H2O.19, H2O.19 CA.15: 5 residues within 4Å: Chain A: D.200, T.407, E.408, Y.464 Ligands: CA.18 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.200, A:D.200, A:E.408, H2O.19, H2O.19 CA.16: 11 residues within 4Å: Chain A: S.259, N.289, Y.290, P.291, V.292, E.329, N.332, D.341, E.384 Ligands: GLY-TYR-THR-ASP.1, CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.290, A:E.329, A:D.341, A:E.384, A:E.384 CA.17: 4 residues within 4Å: Chain A: D.37, S.39, S.86, D.87 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.37, A:S.39, A:S.86, H2O.9, H2O.10 CA.18: 4 residues within 4Å: Chain A: D.200, S.201, T.407 Ligands: CA.15 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.200, A:S.201, A:T.407, H2O.15, H2O.19 CA.19: 2 residues within 4Å: Chain A: T.26, I.27 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.26, H2O.15, H2O.15

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

NA.20: 4 residues within 4Å: Chain A: T.8, N.10, G.31, K.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.10, A:K.32 NA.21: 1 residues within 4Å: Chain A: E.126 No protein-ligand interaction detected (PLIP) NA.22: 2 residues within 4Å: Chain A: E.126, G.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.126, A:E.126, A:G.127

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.23: 10 residues within 4Å: Chain A: Q.362, V.364, R.395, V.397, G.401, Y.402, S.403, L.404, N.455, T.469 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.362, A:R.395, A:R.395 1PE.24: 7 residues within 4Å: Chain A: S.226, G.251, N.252, P.253, S.256, K.257, Q.258 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.258 1PE.25: 8 residues within 4Å: Chain A: N.410, F.412, D.413, L.422, V.428, T.429, S.460, D.461 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.410, A:N.410 1PE.26: 4 residues within 4Å: Chain A: V.40, G.41, T.56, K.58 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, P.L. et al., Molecular basis for a bacterial adhesins peptide-binding module. To Be Published

Release Date

2021-09-01

Peptides

Antifreeze protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Antifreeze protein

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