SMTL ID : 6x6q.1

Peptide-bound structure of Marinomonas primoryensis peptide-binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x ASP- SER- ASP: ASP-SER-ASP(Non-covalent)

ASP-SER-ASP.1: 15 residues within 4Å: Chain A: A.255, Y.291, P.292, V.293, Y.294, S.295, G.296, E.330, T.331, P.332, N.333, D.342, E.385 Ligands: CA.8, CA.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.330 Hydrogen bonds: A:V.293, A:V.293, A:S.295, A:G.296, A:E.330, A:T.331, A:T.331, A:N.333, A:N.333

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

CA.2: 3 residues within 4Å: Chain A: D.77, E.79, F.80 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.77, A:E.79, H2O.6, H2O.13, H2O.15 CA.3: 5 residues within 4Å: Chain A: A.12, I.13, D.17, T.101, H.102 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.17, A:T.101, H2O.3, H2O.12, H2O.15 CA.4: 8 residues within 4Å: Chain A: E.116, R.161, H.163, D.191, S.192, D.426, D.492 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.116, A:R.161, A:D.191, A:D.426, A:D.492 CA.5: 8 residues within 4Å: Chain A: D.191, S.192, A.193, D.426, D.490, D.492, S.494 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.192, A:D.426, A:D.490, A:D.492, A:S.494 CA.6: 5 residues within 4Å: Chain A: D.162, H.163, D.165, V.167, D.169 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.162, A:D.165, A:V.167, A:D.169, H2O.4 CA.7: 6 residues within 4Å: Chain A: V.197, D.199, I.412, N.416, D.421, Y.486 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.197, A:D.199, A:I.412, A:D.421, A:Y.486 CA.8: 10 residues within 4Å: Chain A: S.260, N.290, Y.291, P.292, V.293, E.330, N.333, D.342, E.385 Ligands: ASP-SER-ASP.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:Y.291, A:E.330, A:D.342, A:E.385, A:E.385 CA.9: 7 residues within 4Å: Chain A: N.290, T.331, N.333, S.340, D.342, E.385 Ligands: ASP-SER-ASP.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.331, A:T.331, A:S.340, A:D.342, A:E.385 CA.10: 6 residues within 4Å: Chain A: T.14, D.16, T.18, I.19, D.20, E.23 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.14, A:D.16, A:T.18, A:E.23, H2O.2 CA.11: 3 residues within 4Å: Chain A: D.17, T.101, S.103 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.17, H2O.3, H2O.6, H2O.15 CA.12: 2 residues within 4Å: Chain A: I.22, G.25 No protein-ligand interaction detected (PLIP) CA.13: 5 residues within 4Å: Chain A: D.232, D.241, D.243, S.244 Ligands: CA.14 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.232, A:D.241, A:D.241, H2O.3, H2O.14 CA.14: 7 residues within 4Å: Chain A: D.232, G.233, D.241, D.243, A.245, D.247 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.232, A:D.241, A:D.243, A:A.245, A:D.247 CA.15: 7 residues within 4Å: Chain A: E.214, I.215, A.216, N.242, D.243, D.266, D.268 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.215, A:D.243, A:D.266, A:D.268, H2O.6 CA.16: 4 residues within 4Å: Chain A: D.38, S.40, S.86, S.87 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.38, A:S.40, A:S.87, H2O.9, H2O.13, H2O.15 CA.17: 3 residues within 4Å: Chain A: D.201, S.202, T.408 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.201, A:S.202, A:T.408, H2O.4

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

1PE.18: 8 residues within 4Å: Chain A: V.160, R.161, D.162, A.425, D.426, G.427, S.428, Q.491 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.426, A:S.428 1PE.19: 7 residues within 4Å: Chain A: S.227, G.252, N.253, P.254, S.257, K.258, Q.259 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