SMTL ID : 3gp6.1

Crystal structure of PagP in SDS/MPD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

6 x SDS: DODECYL SULFATE(Non-covalent)

SDS.1: 12 residues within 4Å: Chain A: Y.27, Y.71, M.73, F.75, E.83, I.85, R.115, W.118, L.127, Q.140, N.150, W.157 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.27, A:Y.71, A:Y.71, A:F.75, A:I.85, A:L.127, A:W.157, A:W.157 Salt bridges: A:R.115 SDS.2: 8 residues within 4Å: Chain A: I.14, A.15, W.18, Q.19, F.56, L.70, Y.71 Ligands: MPD.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.14, A:W.18, A:W.18, A:F.56 Hydrogen bonds: A:Q.19 SDS.3: 6 residues within 4Å: Chain A: W.94, P.96, L.104, G.105, S.131, M.141 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.94, A:W.94, A:W.94, A:W.94, A:P.96, A:L.104, A:L.104 Hydrogen bonds: A:R.95 SDS.4: 6 residues within 4Å: Chain A: F.102, V.132, G.133, Y.134, P.136, V.137 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.134, A:P.136, A:V.137 SDS.5: 5 residues within 4Å: Chain A: W.52, A.74, K.76, W.82 Ligands: SO4.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.74, A:W.82, A:W.82 SDS.6: 7 residues within 4Å: Chain A: W.90, S.92, L.106, G.107, P.128 Ligands: MRD.16, SO4.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.90, A:L.106, A:L.106, A:P.128

9 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 1 residues within 4Å: Chain A: D.99 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.99 MPD.8: 5 residues within 4Å: Chain A: I.14, L.70, A.86, G.87, A.110 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.14, A:L.70, A:A.86 MPD.9: 7 residues within 4Å: Chain A: P.21, E.22, H.23, Y.24, L.163 Ligands: SO4.22, LI.23 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.21, A:Y.24, A:Y.24, A:L.163 Hydrogen bonds: A:P.21, A:E.22 MPD.10: 2 residues within 4Å: Chain A: P.124, L.126 No protein-ligand interaction detected (PLIP) MPD.11: 5 residues within 4Å: Chain A: G.54, A.72, M.73, P.84 Ligands: SO4.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.73 MPD.12: 3 residues within 4Å: Chain A: W.118, I.121, L.123 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.118, A:I.121, A:L.123 MPD.13: 2 residues within 4Å: Chain A: A.98, D.99 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.98, A:D.99 MPD.14: 5 residues within 4Å: Chain A: P.84, V.112, T.113, A.114, P.122 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.84, A:V.112, A:A.114, A:P.122 MPD.15: 2 residues within 4Å: Chain A: W.18 Ligands: SDS.2 No protein-ligand interaction detected (PLIP)

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.16: 7 residues within 4Å: Chain A: T.9, F.10, N.13, Y.88, W.90, F.108 Ligands: SDS.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.10, A:W.90, A:F.108 Hydrogen bonds: A:N.13, A:Y.88

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.17: 6 residues within 4Å: Chain A: F.108, L.126, L.127, P.128 Ligands: SDS.6, SO4.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.126 SO4.18: 6 residues within 4Å: Chain A: G.53, G.54, A.74, W.82 Ligands: SDS.5, MPD.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.54, A:G.54, A:A.74 SO4.19: 3 residues within 4Å: Chain A: T.32, F.75, S.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.78 SO4.20: 3 residues within 4Å: Chain A: W.18, L.58 Ligands: SO4.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.18 SO4.21: 4 residues within 4Å: Chain A: P.128, Y.143, P.145 Ligands: SO4.17 No protein-ligand interaction detected (PLIP) SO4.22: 4 residues within 4Å: Chain A: Y.24, L.58 Ligands: MPD.9, SO4.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.24

2 x LI: LITHIUM ION(Non-covalent)

LI.23: 4 residues within 4Å: Chain A: E.22, H.23, L.163 Ligands: MPD.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.22 LI.24: 2 residues within 4Å: Chain A: E.22, R.60 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.22, H2O.1, H2O.1, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuesta-Seijo, J.A. et al., PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler. Structure (2010)

Release Date

2010-06-23

Peptides

Protein pagP: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Protein pagP