SMTL ID : 5ert.1

GephE in complex with Mn(2+) - ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: MN.2, MN.3 25 PLIP interactions: 18 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:S.188, A:E.192, A:D.207, 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:G.309, B:T.96 Water bridges: A:E.192, A:E.192, A:E.192, A:E.192, A:N.310, A:N.310, B:T.96, B:T.96, B:T.96, B:T.96, B:R.141, B:R.141 ADP.10: 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: MN.11, MN.12 25 PLIP interactions: 17 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:S.188, B:D.207, B:D.207, 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:G.309, A:T.96 Water bridges: B:E.192, B:E.192, B:E.192, B:N.310, B:N.310, A:T.96, A:T.96, A:T.96, A:T.96, A:T.96, A:R.141, A:R.141

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: G.190, E.192, D.232, G.256 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MN.3: 5 residues within 4Å: Chain A: G.256, 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.14, H2O.19 MN.11: 5 residues within 4Å: Chain B: G.190, E.192, D.232, G.256 Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MN.12: 5 residues within 4Å: Chain B: G.256, S.258, G.260, D.263 Ligands: ADP.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.263, B:D.263, H2O.1, H2O.6

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

PO4.4: 6 residues within 4Å: Chain A: R.387, L.419 Chain B: R.327, D.334, R.336, T.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.419 Water bridges: A:R.387, A:R.387 Salt bridges: A:R.387 PO4.5: 5 residues within 4Å: Chain A: V.183, R.247, A.248, D.249, K.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.247 Water bridges: A:D.249, A:K.302 Salt bridges: A:K.302 PO4.13: 6 residues within 4Å: Chain A: R.327, D.334, R.336, T.338 Chain B: R.387, L.419 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.419 Water bridges: B:R.387, B:R.387 Salt bridges: B:R.387 PO4.14: 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 Water bridges: B:D.249, B:D.249, B:K.302 Salt bridges: B:K.302

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

ACT.6: 3 residues within 4Å: Chain A: L.6, S.8, F.283 No protein-ligand interaction detected (PLIP) ACT.7: 7 residues within 4Å: Chain A: M.9, D.10, F.13, L.320, I.339, M.394, M.414 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.10 ACT.8: 4 residues within 4Å: Chain A: M.19, T.20, P.21, R.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.20 Salt bridges: A:R.301 ACT.15: 3 residues within 4Å: Chain B: L.6, S.8, F.283 No protein-ligand interaction detected (PLIP) ACT.16: 7 residues within 4Å: Chain B: M.9, D.10, F.13, L.320, I.339, M.394, M.414 No protein-ligand interaction detected (PLIP) ACT.17: 4 residues within 4Å: Chain B: M.19, T.20, P.21, R.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.20 Salt bridges: B:R.301

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

MPD.9: 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.212, A:R.358, B:T.170 MPD.18: 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 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.212, B:R.358, A:T.170

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

Related Entries With Identical Sequence