SMTL ID : 5ers.1

GephE in complex with Mg(2+) - AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 22 residues within 4Å: Chain A: S.188, T.189, E.192, L.193, I.205, R.206, D.207, S.208, N.209, R.210, S.254, G.255, G.256, V.257, S.258, D.263, G.309, N.310, P.311 Chain B: T.96, G.97 Ligands: MG.2 22 PLIP interactions: 17 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.188, A:E.192, A:D.207, A:S.208, A:S.208, A:N.209, A:G.256, A:V.257, A:D.263, A:G.309, B:T.96 Water bridges: A:E.192, A:E.192, A:E.192, A:N.209, A:N.209, A:N.310, A:N.310, B:T.96, B:T.96, B:R.141, B:R.141 AMP.10: 22 residues within 4Å: Chain A: T.96, G.97 Chain B: S.188, T.189, E.192, L.193, I.205, R.206, D.207, S.208, N.209, R.210, S.254, G.255, G.256, V.257, S.258, D.263, G.309, N.310, P.311 Ligands: MG.11 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:S.188, B:D.207, B:D.207, B:S.208, B:S.208, B:N.209, B:G.256, B:V.257, B:D.263, B:G.309, A:T.96 Water bridges: B:E.192, B:N.209, B:N.209, B:N.310, B:N.310, A:T.96, A:T.96, A:T.96, A:G.97, A:R.141, A:R.141

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.190, E.192, G.256 Ligands: AMP.1 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 Ligand-Water interactions Metal complexes: AMP.1, H2O.2, H2O.5, H2O.6, H2O.10, H2O.11 MG.11: 4 residues within 4Å: Chain B: G.190, E.192, G.256 Ligands: AMP.10 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 Ligand-Water interactions Metal complexes: AMP.10, H2O.21, H2O.24, H2O.25, H2O.29, H2O.30

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

ACT.3: 4 residues within 4Å: Chain A: T.25, A.39, K.156, N.179 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.25, A:A.39 ACT.4: 3 residues within 4Å: Chain A: L.6, S.8, F.283 No protein-ligand interaction detected (PLIP) ACT.5: 4 residues within 4Å: Chain A: C.152, V.153, L.154, A.155 No protein-ligand interaction detected (PLIP) ACT.12: 4 residues within 4Å: Chain B: T.25, A.39, K.156, N.179 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.25, B:A.39 ACT.13: 3 residues within 4Å: Chain B: L.6, S.8, F.283 No protein-ligand interaction detected (PLIP) ACT.14: 4 residues within 4Å: Chain B: C.152, V.153, L.154, A.155 No protein-ligand interaction detected (PLIP)

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 5 residues within 4Å: Chain A: V.183, R.247, A.248, D.249, K.302 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.246, A:D.249, A:D.249 Water bridges: A:K.302, A:K.302 Salt bridges: A:K.302 PO4.15: 5 residues within 4Å: Chain B: V.183, R.247, A.248, D.249, K.302 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.246, B:D.249, B:D.249 Water bridges: B:K.302, B:K.302 Salt bridges: B:K.302

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

MPD.7: 12 residues within 4Å: Chain A: L.48, I.147, S.163, G.166, L.167, T.170 Chain B: S.208, T.212, P.311, V.312, V.315, R.358 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.212, B:V.312 Hydrogen bonds: B:R.358, B:R.358 MPD.8: 6 residues within 4Å: Chain A: N.195, P.196, E.197, R.210, N.226 Chain B: R.31 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:E.197 Water bridges: A:R.210, A:R.210, A:N.226 Hydrogen bonds: B:R.31 MPD.9: 10 residues within 4Å: Chain A: M.9, D.10, F.13, L.320, R.336, P.337, I.339, Y.356, M.394, M.414 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.13, A:F.13, A:F.13, A:I.339 MPD.16: 12 residues within 4Å: Chain A: S.208, T.212, P.311, V.312, V.315, R.358 Chain B: L.48, I.147, S.163, G.166, L.167, T.170 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.212, A:V.312 Hydrogen bonds: A:R.358, A:R.358 MPD.17: 6 residues within 4Å: Chain A: R.31 Chain B: N.195, P.196, E.197, R.210, N.226 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.31 Hydrophobic interactions: B:E.197 Water bridges: B:R.210, B:R.210, B:N.226 MPD.18: 10 residues within 4Å: Chain B: M.9, D.10, F.13, L.320, R.336, P.337, I.339, Y.356, M.394, M.414 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.13, B:F.13, B:F.13, B:I.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis. Structure (2016)

Release Date

2016-05-04

Peptides

Gephyrin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Gephyrin

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