SMTL ID : 5erq.1

Gephyrin E domain at 1.55 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 3 residues within 4Å: Chain A: L.6, S.8, F.283 Ligand excluded by PLIP ACT.2: 7 residues within 4Å: Chain A: R.382, S.385, M.386 Chain B: C.152, V.153, L.154, A.155 Ligand excluded by PLIP ACT.3: 7 residues within 4Å: Chain A: M.9, F.13, L.320, P.337, I.339, M.394, M.414 Ligand excluded by PLIP ACT.4: 5 residues within 4Å: Chain A: V.183, R.247, A.248, D.249, K.302 Ligand excluded by PLIP ACT.5: 7 residues within 4Å: Chain A: E.18, M.19, T.20, P.21, V.22, R.301, K.328 Ligand excluded by PLIP ACT.6: 3 residues within 4Å: Chain A: T.25, A.39, K.156 Ligand excluded by PLIP ACT.7: 4 residues within 4Å: Chain A: D.296, G.299, V.300, R.301 Ligand excluded by PLIP ACT.8: 4 residues within 4Å: Chain A: I.147, V.153, L.167 Ligands: MPD.23 Ligand excluded by PLIP ACT.9: 5 residues within 4Å: Chain A: K.285, V.348, E.355, H.357, L.395 Ligand excluded by PLIP ACT.10: 4 residues within 4Å: Chain A: L.6, F.283, L.288, R.353 Ligand excluded by PLIP ACT.13: 3 residues within 4Å: Chain B: L.6, S.8, F.283 Ligand excluded by PLIP ACT.14: 7 residues within 4Å: Chain A: C.152, V.153, L.154, A.155 Chain B: R.382, S.385, M.386 Ligand excluded by PLIP ACT.15: 7 residues within 4Å: Chain B: M.9, F.13, L.320, P.337, I.339, M.394, M.414 Ligand excluded by PLIP ACT.16: 5 residues within 4Å: Chain B: V.183, R.247, A.248, D.249, K.302 Ligand excluded by PLIP ACT.17: 7 residues within 4Å: Chain B: E.18, M.19, T.20, P.21, V.22, R.301, K.328 Ligand excluded by PLIP ACT.18: 3 residues within 4Å: Chain B: T.25, A.39, K.156 Ligand excluded by PLIP ACT.19: 4 residues within 4Å: Chain B: D.296, G.299, V.300, R.301 Ligand excluded by PLIP ACT.20: 4 residues within 4Å: Chain B: I.147, V.153, L.167 Ligands: MPD.11 Ligand excluded by PLIP ACT.21: 5 residues within 4Å: Chain B: K.285, V.348, E.355, H.357, L.395 Ligand excluded by PLIP ACT.22: 4 residues within 4Å: Chain B: L.6, F.283, L.288, R.353 Ligand excluded by PLIP

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

MPD.11: 12 residues within 4Å: Chain A: S.208, T.212, P.311, V.312, V.315, R.358 Chain B: I.147, S.163, G.166, L.167, T.170 Ligands: ACT.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.311 Hydrogen bonds: A:R.358, A:R.358 Water bridges: A:S.208 MPD.12: 8 residues within 4Å: Chain A: P.52, I.100, P.101, C.102, G.103, A.104, D.105, I.140 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.52 Hydrogen bonds: A:G.103, A:A.104, A:A.104 Water bridges: A:A.104 MPD.23: 12 residues within 4Å: Chain A: I.147, S.163, G.166, L.167, T.170 Chain B: S.208, T.212, P.311, V.312, V.315, R.358 Ligands: ACT.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.311 Hydrogen bonds: B:R.358, B:R.358 Water bridges: B:S.208 MPD.24: 8 residues within 4Å: Chain B: P.52, I.100, P.101, C.102, G.103, A.104, D.105, I.140 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.52 Hydrogen bonds: B:G.103, B:A.104, B:A.104 Water bridges: B:A.104

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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