SMTL ID : 5vf2.1

scFv 2D10 re-refined as a complex with trehalose replacing the original alpha-1,6-mannobiose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 1 residues within 4Å: Chain A: Y.102 No protein-ligand interaction detected (PLIP) GLC-GLC.2: 5 residues within 4Å: Chain A: V.169, H.170, S.171, T.236, H.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.171

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 5 residues within 4Å: Chain A: Y.103, Y.193, R.198, F.199, S.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.200

41 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 4 residues within 4Å: Chain A: Y.102 Ligands: UNX.5, UNX.6, UNX.15 Ligand excluded by PLIP UNX.5: 6 residues within 4Å: Chain A: Y.102, N.172 Ligands: UNX.4, UNX.6, UNX.8, UNX.15 Ligand excluded by PLIP UNX.6: 5 residues within 4Å: Chain A: N.172 Ligands: UNX.4, UNX.5, UNX.8, UNX.15 Ligand excluded by PLIP UNX.7: 6 residues within 4Å: Chain A: K.100, Y.102, S.105 Ligands: UNX.17, UNX.32, UNX.43 Ligand excluded by PLIP UNX.8: 7 residues within 4Å: Chain A: N.172, Y.176 Ligands: UNX.5, UNX.6, UNX.15, UNX.32, UNX.43 Ligand excluded by PLIP UNX.9: 9 residues within 4Å: Chain A: Y.61, K.66, G.67, A.69 Ligands: UNX.10, UNX.11, UNX.12, UNX.16, UNX.24 Ligand excluded by PLIP UNX.10: 7 residues within 4Å: Chain A: Y.61, K.66 Ligands: UNX.9, UNX.12, UNX.16, UNX.24, UNX.26 Ligand excluded by PLIP UNX.11: 6 residues within 4Å: Chain A: A.69, T.70 Ligands: UNX.9, UNX.14, UNX.16, UNX.24 Ligand excluded by PLIP UNX.12: 10 residues within 4Å: Chain A: K.66, G.67 Ligands: UNX.9, UNX.10, UNX.13, UNX.14, UNX.16, UNX.24, UNX.25, UNX.26 Ligand excluded by PLIP UNX.13: 4 residues within 4Å: Ligands: UNX.12, UNX.14, UNX.16, UNX.26 Ligand excluded by PLIP UNX.14: 5 residues within 4Å: Chain A: G.67 Ligands: UNX.11, UNX.12, UNX.13, UNX.16 Ligand excluded by PLIP UNX.15: 5 residues within 4Å: Chain A: N.172 Ligands: UNX.4, UNX.5, UNX.6, UNX.8 Ligand excluded by PLIP UNX.16: 8 residues within 4Å: Ligands: UNX.9, UNX.10, UNX.11, UNX.12, UNX.13, UNX.14, UNX.24, UNX.26 Ligand excluded by PLIP UNX.17: 5 residues within 4Å: Chain A: Y.102 Ligands: UNX.7, UNX.29, UNX.32, UNX.44 Ligand excluded by PLIP UNX.18: 4 residues within 4Å: Ligands: UNX.19, UNX.20, UNX.41, UNX.42 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Ligands: UNX.18, UNX.20, UNX.42 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Ligands: UNX.18, UNX.19, UNX.42 Ligand excluded by PLIP UNX.21: 4 residues within 4Å: Chain A: S.8, G.9 Ligands: UNX.22, UNX.23 Ligand excluded by PLIP UNX.22: 3 residues within 4Å: Chain A: G.9 Ligands: UNX.21, UNX.23 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain A: G.9 Ligands: UNX.21, UNX.22 Ligand excluded by PLIP UNX.24: 9 residues within 4Å: Chain A: F.65, K.66, G.67, A.69 Ligands: UNX.9, UNX.10, UNX.11, UNX.12, UNX.16 Ligand excluded by PLIP UNX.25: 3 residues within 4Å: Chain A: K.66 Ligands: UNX.12, UNX.26 Ligand excluded by PLIP UNX.26: 6 residues within 4Å: Chain A: K.66 Ligands: UNX.10, UNX.12, UNX.13, UNX.16, UNX.25 Ligand excluded by PLIP UNX.27: 4 residues within 4Å: Chain A: D.74, K.75, S.76 Ligands: UNX.28 Ligand excluded by PLIP UNX.28: 4 residues within 4Å: Chain A: V.73, D.74, K.75 Ligands: UNX.27 Ligand excluded by PLIP UNX.29: 5 residues within 4Å: Ligands: UNX.17, UNX.30, UNX.31, UNX.32, UNX.44 Ligand excluded by PLIP UNX.30: 4 residues within 4Å: Chain A: V.238, Y.240 Ligands: UNX.29, UNX.31 Ligand excluded by PLIP UNX.31: 4 residues within 4Å: Chain A: Y.240 Ligands: UNX.29, UNX.30, UNX.44 Ligand excluded by PLIP UNX.32: 5 residues within 4Å: Ligands: UNX.7, UNX.8, UNX.17, UNX.29, UNX.43 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain A: P.147, F.148 Ligand excluded by PLIP UNX.34: 4 residues within 4Å: Chain A: P.203, D.204 Ligands: UNX.35, UNX.42 Ligand excluded by PLIP UNX.35: 3 residues within 4Å: Chain A: D.204, R.205 Ligands: UNX.34 Ligand excluded by PLIP UNX.36: 2 residues within 4Å: Chain A: R.198 Ligands: UNX.39 Ligand excluded by PLIP UNX.37: 3 residues within 4Å: Chain A: R.198 Ligands: UNX.38, UNX.39 Ligand excluded by PLIP UNX.38: 1 residues within 4Å: Ligands: UNX.37 Ligand excluded by PLIP UNX.39: 2 residues within 4Å: Ligands: UNX.36, UNX.37 Ligand excluded by PLIP UNX.40: 2 residues within 4Å: Chain A: S.60, Y.61 Ligand excluded by PLIP UNX.41: 4 residues within 4Å: Chain A: R.205, E.223 Ligands: UNX.18, UNX.42 Ligand excluded by PLIP UNX.42: 5 residues within 4Å: Ligands: UNX.18, UNX.19, UNX.20, UNX.34, UNX.41 Ligand excluded by PLIP UNX.43: 5 residues within 4Å: Chain A: H.170, Y.176 Ligands: UNX.7, UNX.8, UNX.32 Ligand excluded by PLIP UNX.44: 3 residues within 4Å: Ligands: UNX.17, UNX.29, UNX.31 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.45: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wlodawer, A. et al., Detect, correct, retract: How to manage incorrect structural models. FEBS J. (2018)

Release Date

2017-12-06

Peptides

scFv 2D10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

scFv 2D10

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