SMTL ID : 5err.1

GephE in complex with Mg(2+) - ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 26 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, P.289, P.308, G.309, N.310, P.311 Chain B: T.96, G.97, R.141 Ligands: MG.2, MG.3 28 PLIP interactions: 8 interactions with chain B, 20 interactions with chain A Water bridges: B:T.96, B:T.96, B:T.96, B:T.96, B:T.96, B:G.97, B:R.141, B:R.141, A:E.192, A:N.209, A:N.209, A:D.263, A:D.263, A:N.310, A:N.310 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:S.258, A:S.258, A:S.258, A:S.258, A:G.309 ADP.14: 26 residues within 4Å: Chain A: T.96, G.97, R.141 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, P.289, P.308, G.309, N.310, P.311 Ligands: MG.15, MG.16 26 PLIP interactions: 17 interactions with chain B, 9 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:S.258, B:S.258, B:S.258, B:S.258, B:G.309 Water bridges: B:N.209, B:N.209, B:N.310, B:N.310, A:T.96, A:T.96, A:T.96, A:T.96, A:T.96, A:G.97, A:G.97, A:R.141, A:R.141

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.190, E.192, G.256 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: S.258, G.260, D.263 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.263, A:D.263, H2O.27, H2O.28 MG.15: 4 residues within 4Å: Chain B: G.190, E.192, G.256 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain B: S.258, G.260, D.263 Ligands: ADP.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.263, B:D.263, H2O.9, H2O.10

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

ACT.4: 6 residues within 4Å: Chain A: M.9, D.10, F.13, I.339, M.394, M.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.10 Water bridges: A:Y.356 ACT.5: 3 residues within 4Å: Chain A: L.6, S.8, F.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.6 ACT.6: 7 residues within 4Å: Chain A: L.344, S.345, C.346, A.372, Q.373, S.374, L.393 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.374 ACT.7: 6 residues within 4Å: Chain A: M.19, T.20, P.21, V.22, R.301, K.328 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.301 ACT.17: 6 residues within 4Å: Chain B: M.9, D.10, F.13, I.339, M.394, M.414 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.356 ACT.18: 3 residues within 4Å: Chain B: L.6, S.8, F.283 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.6 ACT.19: 7 residues within 4Å: Chain B: L.344, S.345, C.346, A.372, Q.373, S.374, L.393 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.374 ACT.20: 6 residues within 4Å: Chain B: M.19, T.20, P.21, V.22, R.301, K.328 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.301

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

MPD.8: 9 residues within 4Å: Chain A: H.159, R.327, I.332, T.338 Chain B: I.360, R.387, N.390, R.418, L.419 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:H.159, B:R.387 Hydrogen bonds: A:R.327, A:R.327, B:R.387, B:R.387, B:N.390 Water bridges: A:D.334, A:T.338, B:L.419 MPD.9: 6 residues within 4Å: Chain A: C.152, V.153, L.154, A.155 Chain B: R.382, S.385 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.152, A:V.153 MPD.10: 4 residues within 4Å: Chain A: N.195, E.197, R.210 Chain B: R.31 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.195 MPD.11: 11 residues within 4Å: Chain A: S.208, T.212, P.311, V.312, V.315, R.358 Chain B: L.48, S.163, G.166, L.167, T.170 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.208, A:R.358, A:R.358 Water bridges: A:T.212 MPD.12: 7 residues within 4Å: Chain A: K.285, P.286, G.287, L.288, P.289, S.313, R.353 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.288 Hydrogen bonds: A:G.287, A:L.288, A:R.353 Water bridges: A:S.313, A:S.313 MPD.21: 9 residues within 4Å: Chain A: I.360, R.387, N.390, R.418, L.419 Chain B: H.159, R.327, I.332, T.338 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:R.387, B:H.159 Hydrogen bonds: A:R.387, A:R.387, A:N.390, B:R.327, B:R.327 Water bridges: B:D.334, B:T.338, B:T.338 MPD.22: 6 residues within 4Å: Chain A: R.382, S.385 Chain B: C.152, V.153, L.154, A.155 2 PLIP interactions: 2 interactions with chain B Water bridges: B:C.152, B:V.153 MPD.23: 4 residues within 4Å: Chain A: R.31 Chain B: N.195, E.197, R.210 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.195 MPD.24: 11 residues within 4Å: Chain A: L.48, 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 Hydrogen bonds: B:S.208, B:R.358, B:R.358 Water bridges: B:T.212 MPD.25: 7 residues within 4Å: Chain B: K.285, P.286, G.287, L.288, P.289, S.313, R.353 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.288 Hydrogen bonds: B:G.287, B:L.288, B:R.353 Water bridges: B:S.313, B:S.313

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

PO4.13: 5 residues within 4Å: Chain A: V.183, R.247, A.248, D.249, K.302 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.247, A:R.247 Water bridges: A:K.302, A:K.302 Salt bridges: A:K.302 PO4.26: 5 residues within 4Å: Chain B: V.183, R.247, A.248, D.249, K.302 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.247, B:R.247 Water bridges: B:K.302, B:K.302 Salt bridges: B:K.302

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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