SMTL ID : 3l22.1

CRYSTAL STRUCTURE OF A SUSD SUPERFAMILY PROTEIN (BF_0597) FROM BACTEROIDES FRAGILIS AT 2.05 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 2 residues within 4Å: Chain A: E.119, H.197 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.119, A:E.119, A:H.197, H2O.6, H2O.7 ZN.2: 3 residues within 4Å: Chain A: E.107 Ligands: ACT.17, ACT.18 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.107, A:E.107 ZN.3: 1 residues within 4Å: Chain A: E.234 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.234, H2O.2, H2O.2, H2O.2, H2O.2, H2O.16 ZN.4: 3 residues within 4Å: Chain A: D.186, E.188 Ligands: ACT.13 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.186, A:E.188, ACT.13 ZN.5: 2 residues within 4Å: Chain A: H.405 Ligands: ACT.12 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.405, H2O.2, ACT.12 ZN.6: 1 residues within 4Å: Chain A: D.114 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.114, H2O.1, H2O.7, H2O.8, H2O.23 ZN.7: 2 residues within 4Å: Chain A: H.174 Ligands: ACT.10 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.174, ACT.10, H2O.19 ZN.8: 1 residues within 4Å: Ligands: EDO.20 No protein-ligand interaction detected (PLIP) ZN.9: 1 residues within 4Å: Chain A: D.290 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.290, H2O.13, H2O.15

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 4 residues within 4Å: Chain A: L.150, L.152, H.174 Ligands: ZN.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.150, A:L.152 Salt bridges: A:H.174 ACT.11: 4 residues within 4Å: Chain A: K.297, G.357, R.358 Ligands: ACT.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.357 Water bridges: A:K.297 Salt bridges: A:K.297 ACT.12: 5 residues within 4Å: Chain A: H.405, G.418, P.419, S.420 Ligands: ZN.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.420 Water bridges: A:G.418 Salt bridges: A:H.405 ACT.13: 4 residues within 4Å: Chain A: R.115, D.186, E.188 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.115, A:T.187 Salt bridges: A:R.115 ACT.14: 3 residues within 4Å: Chain A: E.234, D.235, K.297 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.234 Salt bridges: A:K.297 ACT.15: 4 residues within 4Å: Chain A: T.295, K.297, I.300 Ligands: ACT.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.300 Water bridges: A:T.295 ACT.16: 4 residues within 4Å: Chain A: N.215, E.216, W.217, D.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.217, A:D.218 Water bridges: A:K.219 ACT.17: 4 residues within 4Å: Chain A: E.107 Ligands: ZN.2, ACT.18, EDO.23 No protein-ligand interaction detected (PLIP) ACT.18: 3 residues within 4Å: Chain A: E.107 Ligands: ZN.2, ACT.17 No protein-ligand interaction detected (PLIP)

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

EDO.19: 6 residues within 4Å: Chain A: E.225, L.334, Y.338, T.347, L.351 Ligands: EDO.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.225 Water bridges: A:Y.338 EDO.20: 1 residues within 4Å: Ligands: ZN.8 No protein-ligand interaction detected (PLIP) EDO.21: 4 residues within 4Å: Chain A: A.342, G.343, G.344, E.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.343, A:G.343, A:E.345 Water bridges: A:A.346 EDO.22: 8 residues within 4Å: Chain A: Y.129, R.209, E.329, D.333, K.385, I.397, D.398, R.401 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.129, A:Y.129, A:D.333, A:K.385 EDO.23: 2 residues within 4Å: Chain A: E.107 Ligands: ACT.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.104 EDO.24: 6 residues within 4Å: Chain A: T.237, Y.240, A.301, F.302, M.310, K.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.301 Water bridges: A:Q.320, A:Q.320 EDO.25: 5 residues within 4Å: Chain A: L.176, L.179, E.180, K.207, Y.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.176, A:K.207 EDO.26: 5 residues within 4Å: Chain A: E.225, Y.327, L.331, L.334 Ligands: EDO.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.327 EDO.27: 5 residues within 4Å: Chain A: N.371, L.372, S.373, D.375, A.376 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.371, A:S.373, A:D.375, A:A.376 Water bridges: A:D.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of SusD superfamily protein (YP_210307.1) from Bacteroides fragilis NCTC 9343 at 2.05 A resolution. To be published

Release Date

2010-01-12

Peptides

SusD superfamily protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SusD superfamily protein