SMTL ID : 2gpj.1

CRYSTAL STRUCTURE OF A SIDEROPHORE-INTERACTING PROTEIN (SPUTCN32_0076) FROM SHEWANELLA PUTREFACIENS CN-32 AT 2.20 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: G.140, H.160, E.162 No protein-ligand interaction detected (PLIP) CA.2: 4 residues within 4Å: Chain A: H.209, A.213, H.214 Ligands: ACY.18 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.209

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.207, K.211 Ligand excluded by PLIP

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.4: 27 residues within 4Å: Chain A: R.59, T.60, Y.61, T.62, D.74, F.75, V.76, H.78, D.79, T.80, G.82, P.83, A.84, S.85, T.122, P.125, Y.226, W.227, K.228, G.230, C.231, N.232, E.233, K.240 Ligands: EDO.9, ACY.13, ACY.14 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:T.60, A:Y.226, A:Y.226, A:Y.226 Hydrogen bonds: A:T.60, A:T.60, A:Y.61, A:T.62, A:D.74, A:V.76, A:G.82, A:A.84, A:S.85, A:G.230, A:C.231, A:C.231, A:E.233 Water bridges: A:R.59, A:R.59, A:Y.61, A:T.62, A:T.62, A:Y.226, A:K.228 Salt bridges: A:R.59, A:R.59, A:H.78 pi-Stacking: A:H.78, A:H.78, A:Y.226, A:W.227

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

EDO.5: 3 residues within 4Å: Chain A: A.38, D.39, Q.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.39 Water bridges: A:E.41 EDO.6: 9 residues within 4Å: Chain A: M.23, R.25, R.64, D.74, L.124, P.125, S.128, Q.153, L.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.64, A:S.128, A:Q.153 Water bridges: A:Q.153 EDO.7: 4 residues within 4Å: Chain A: L.155, V.156, H.157, E.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.155, A:H.157 EDO.8: 4 residues within 4Å: Chain A: L.57, M.58, R.59, E.233 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.59, A:E.233 EDO.9: 7 residues within 4Å: Chain A: H.78, D.79, L.147, P.169, A.171 Ligands: FAD.4, ACY.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.79, A:A.171 EDO.10: 3 residues within 4Å: Chain A: N.201, K.228, I.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.201, A:K.228, A:I.229 EDO.11: 2 residues within 4Å: Chain A: N.109, E.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.109, A:E.111 EDO.12: 6 residues within 4Å: Chain A: L.48, P.50, W.87, L.96, I.97, Q.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.87, A:Q.98

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.13: 7 residues within 4Å: Chain A: D.120, M.121, T.122, L.147, W.227 Ligands: FAD.4, EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.122 ACY.14: 8 residues within 4Å: Chain A: K.46, T.60, E.233, H.236, K.237, K.240 Ligands: FAD.4, ACY.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.240 Hydrogen bonds: A:T.60 Water bridges: A:H.236 Salt bridges: A:K.46, A:H.236, A:K.237, A:K.240 ACY.15: 3 residues within 4Å: Chain A: R.181, Q.184, L.185 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.184, A:L.185 ACY.16: 5 residues within 4Å: Chain A: K.237, K.240, Q.241, E.244 Ligands: ACY.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.240 Hydrogen bonds: A:Q.241 Salt bridges: A:K.237, A:K.240 ACY.17: 4 residues within 4Å: Chain A: D.113, V.139, L.188, A.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.189 ACY.18: 5 residues within 4Å: Chain A: I.182, L.185, W.187, H.209 Ligands: CA.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.187 Salt bridges: A:H.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of siderophore-interacting protein (ZP_00813641.1) from Shewanella putrefaciens CN-32 at 2.20 A resolution. To be published

Release Date

2006-06-13

Peptides

Siderophore-interacting protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Siderophore-interacting protein