SMTL ID : 4ka9.1

Crystal structure analysis of single amino acid deletion mutations in EGFP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: P.87, F.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.87 EDO.2: 3 residues within 4Å: Chain A: Q.202, V.222, T.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.223 Water bridges: A:S.200, A:Q.202, A:V.222 EDO.3: 5 residues within 4Å: Chain A: R.107, A.108, E.109, R.120, E.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.107, A:R.107 EDO.4: 2 residues within 4Å: Chain A: G.114, D.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.115 EDO.5: 5 residues within 4Å: Chain A: V.11, E.34, D.36, K.41, T.43 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.34, A:K.41 EDO.6: 5 residues within 4Å: Chain A: E.93, R.94, T.95, T.106 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.95, A:T.106 EDO.7: 4 residues within 4Å: Chain A: E.32, G.33, E.34, T.43 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.32, A:E.34, A:K.45 EDO.8: 5 residues within 4Å: Chain A: K.105, R.107, E.122, K.124 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.9: 6 residues within 4Å: Chain A: H.146, N.147, Y.149, F.163, K.164, R.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.147, A:N.147, A:K.164 Water bridges: A:S.145, A:R.166

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 6 residues within 4Å: Chain A: D.74, H.75, M.76, K.77, Q.78, L.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.77, A:Q.78, A:Q.78 Water bridges: A:Q.78

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 2 residues within 4Å: Chain A: H.25, E.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.25 NA.14: 1 residues within 4Å: Chain A: K.4 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.12: 2 residues within 4Å: Chain A: D.195, M.231 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.195, A:M.231, H2O.8 ZN.13: 2 residues within 4Å: Chain A: D.74, H.75 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.74, A:H.75, H2O.7, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arpino, J.A. et al., Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure. Structure (2014)

Release Date

2014-05-07

Peptides

Green fluorescent protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Green fluorescent protein