SMTL ID : 5erv.1

Ternary complex of GephE - ADP - Tungsten cluster

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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, CA.14 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.188, A:D.207, A:D.207, A:S.208, A:S.208, A:N.209, A:G.255, A:G.256, A:V.257, A:S.258, A:S.258, A:S.258, A:S.258, A:G.309, B:R.141 Water bridges: A:E.192, A:E.192, A:D.263, A:N.310, B:T.96, B:T.96, B:T.96, B:G.97, B:G.97 ADP.17: 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.18, CA.30 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.188, B:E.192, B:D.207, B:S.208, B:S.208, B:N.209, B:G.255, B:G.256, B:V.257, B:S.258, B:S.258, B:S.258, B:S.258, B:G.309, A:R.141 Water bridges: B:E.192, B:E.192, B:N.310, A:T.96, A:T.96, A:T.96, A:G.97, A:G.97

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.258, D.263 Chain B: T.96 Ligands: ADP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.263, A:D.263, H2O.5, H2O.11, H2O.19 MG.18: 4 residues within 4Å: Chain A: T.96 Chain B: S.258, D.263 Ligands: ADP.17 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.263, B:D.263, H2O.4, H2O.20, H2O.25

18 x W: TUNGSTEN ION(Non-covalent)(Non-functional Binders)

W.3: 3 residues within 4Å: Chain B: K.56 Ligands: W.10, W.11 Ligand excluded by PLIP W.4: 9 residues within 4Å: Chain A: P.286, G.287, L.288, R.353 Ligands: W.7, W.9, W.10, W.11, WO4.16 Ligand excluded by PLIP W.5: 5 residues within 4Å: Chain B: V.55, K.56 Ligands: W.6, W.7, W.11 Ligand excluded by PLIP W.6: 4 residues within 4Å: Chain A: K.285 Ligands: W.5, W.9, W.11 Ligand excluded by PLIP W.7: 6 residues within 4Å: Ligands: W.4, W.5, W.8, W.9, W.11, WO4.16 Ligand excluded by PLIP W.8: 2 residues within 4Å: Ligands: W.7, WO4.16 Ligand excluded by PLIP W.9: 7 residues within 4Å: Chain A: K.285, P.286 Ligands: W.4, W.6, W.7, W.11, WO4.16 Ligand excluded by PLIP W.10: 5 residues within 4Å: Chain A: L.288, R.353 Ligands: W.3, W.4, W.11 Ligand excluded by PLIP W.11: 8 residues within 4Å: Chain A: R.353 Ligands: W.3, W.4, W.5, W.6, W.7, W.9, W.10 Ligand excluded by PLIP W.19: 3 residues within 4Å: Chain A: K.56 Ligands: W.26, W.27 Ligand excluded by PLIP W.20: 9 residues within 4Å: Chain B: P.286, G.287, L.288, R.353 Ligands: W.23, W.25, W.26, W.27, WO4.32 Ligand excluded by PLIP W.21: 5 residues within 4Å: Chain A: V.55, K.56 Ligands: W.22, W.23, W.27 Ligand excluded by PLIP W.22: 4 residues within 4Å: Chain B: K.285 Ligands: W.21, W.25, W.27 Ligand excluded by PLIP W.23: 6 residues within 4Å: Ligands: W.20, W.21, W.24, W.25, W.27, WO4.32 Ligand excluded by PLIP W.24: 2 residues within 4Å: Ligands: W.23, WO4.32 Ligand excluded by PLIP W.25: 7 residues within 4Å: Chain B: K.285, P.286 Ligands: W.20, W.22, W.23, W.27, WO4.32 Ligand excluded by PLIP W.26: 5 residues within 4Å: Chain B: L.288, R.353 Ligands: W.19, W.20, W.27 Ligand excluded by PLIP W.27: 8 residues within 4Å: Chain B: R.353 Ligands: W.19, W.20, W.21, W.22, W.23, W.25, W.26 Ligand excluded by PLIP

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

ACT.12: 5 residues within 4Å: Chain A: C.152, V.153, L.154, A.155 Chain B: S.385 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.385, B:S.385 ACT.13: 6 residues within 4Å: Chain A: V.183, S.246, R.247, A.248, D.249, K.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.247 Salt bridges: A:K.302 ACT.28: 5 residues within 4Å: Chain A: S.385 Chain B: C.152, V.153, L.154, A.155 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.385, A:S.385 ACT.29: 6 residues within 4Å: Chain B: V.183, S.246, R.247, A.248, D.249, K.302 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.247 Salt bridges: B:K.302

2 x CA: CALCIUM ION(Non-functional Binders)

CA.14: 2 residues within 4Å: Chain A: G.256 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) CA.30: 2 residues within 4Å: Chain B: G.256 Ligands: ADP.17 No protein-ligand interaction detected (PLIP)

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

MPD.15: 4 residues within 4Å: Chain A: R.31 Chain B: N.195, E.197, R.210 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.197, B:E.197, A:R.31, A:R.31 Water bridges: B:R.210 MPD.31: 4 residues within 4Å: Chain A: N.195, E.197, R.210 Chain B: R.31 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.31, B:R.31, A:E.197, A:E.197 Water bridges: A:R.210

2 x WO4: TUNGSTATE(VI)ION(Non-covalent)

WO4.16: 11 residues within 4Å: Chain A: P.286, G.287, L.288, P.289, P.308, N.310, S.313 Ligands: W.4, W.7, W.8, W.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.287, A:L.288, A:S.313 Water bridges: A:N.310, A:N.310 WO4.32: 11 residues within 4Å: Chain B: P.286, G.287, L.288, P.289, P.308, N.310, S.313 Ligands: W.20, W.23, W.24, W.25 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.287, B:L.288, B:S.313 Water bridges: B:N.310, B:N.310

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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