SMTL ID : 3qpx.1

Crystal structure of Fab C2507

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-oligomer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: P.59, S.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.60 SO4.2: 4 residues within 4Å: Chain A: S.9, A.99, G.100 Ligands: SO4.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.100 SO4.3: 2 residues within 4Å: Chain A: R.107, T.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.107, A:T.108 Water bridges: A:R.107 SO4.4: 4 residues within 4Å: Chain A: D.1, I.2, Q.27 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.27, A:Q.27, A:S.93 SO4.17: 3 residues within 4Å: Chain B: Q.177, S.178, S.179 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.179, B:S.179 Water bridges: B:K.149, B:Q.177, B:Q.177, B:S.178, B:S.178, B:S.178 SO4.18: 3 residues within 4Å: Chain B: W.33, T.101, R.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.102 Water bridges: B:T.101 Salt bridges: B:R.102 SO4.19: 3 residues within 4Å: Chain B: P.41, G.42 Ligands: SO4.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.42 Water bridges: B:G.44 SO4.20: 4 residues within 4Å: Chain B: S.134, K.135, C.222, H.223 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.134, B:C.222 Water bridges: B:K.135, B:K.135, B:K.135 Salt bridges: B:K.135, B:H.223 SO4.21: 3 residues within 4Å: Chain B: H.225, H.226, H.227 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:K.189, A:K.189, A:N.209 Salt bridges: A:K.189, B:H.227 Hydrogen bonds: B:H.227 SO4.22: 6 residues within 4Å: Chain B: M.93, V.113, T.114, P.155, K.207 Ligands: GOL.25 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.114, B:T.114 Water bridges: B:P.155, B:T.157, B:N.205 Salt bridges: B:K.207 SO4.23: 4 residues within 4Å: Chain B: L.27, T.28, A.31, N.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:N.32 Water bridges: B:R.98

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: P.8, S.9, L.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.9, A:L.10, A:L.10 Water bridges: A:S.9, A:S.9 GOL.6: 7 residues within 4Å: Chain A: Q.37, K.45, P.59, R.61, F.62, E.81, D.82 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.37, A:K.45, A:K.45, A:R.61, A:E.81, A:D.82 GOL.7: 4 residues within 4Å: Chain A: N.92, S.93, R.94 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.94 Water bridges: A:D.95 GOL.8: 3 residues within 4Å: Chain A: D.1, Q.3 Ligands: GOL.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.46 GOL.9: 5 residues within 4Å: Chain A: D.1, S.93, R.94 Ligands: SO4.4, GOL.7 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:D.62, B:D.62, A:D.1 Hydrogen bonds: A:D.1, A:R.94 GOL.10: 4 residues within 4Å: Chain A: H.197, Q.198, L.200, S.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.197 Water bridges: A:H.197 GOL.11: 10 residues within 4Å: Chain A: Q.159, S.161, S.175, S.176, T.177 Chain B: F.172, P.173, S.183, L.184, S.185 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.172, B:S.185, B:S.185, A:Q.159, A:S.161 Water bridges: A:T.177 GOL.12: 6 residues within 4Å: Chain A: T.163, E.164, D.166, T.171 Chain B: V.169, H.170 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.165, A:D.166, A:T.171, B:V.169 Water bridges: B:T.171 GOL.24: 7 residues within 4Å: Chain A: F.97, G.98, A.99 Chain B: K.43, G.44, L.45 Ligands: GOL.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.97, B:L.45, B:L.45 Water bridges: A:F.97 GOL.25: 5 residues within 4Å: Chain B: Q.111, G.112, V.113, K.207 Ligands: SO4.22 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.111, B:K.207, B:K.207 Water bridges: B:G.112, B:T.157

6 x CD: CADMIUM ION(Non-covalent)

CD.13: 2 residues within 4Å: Chain A: D.150, H.188 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.150, A:H.188 CD.14: 3 residues within 4Å: Chain A: N.136, N.137 Chain B: H.170 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.170, H2O.35, H2O.383 CD.15: 1 residues within 4Å: Chain A: D.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.1, A:D.1, H2O.96 CD.26: 1 residues within 4Å: Chain B: H.224 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.224 CD.27: 3 residues within 4Å: Chain A: E.212 Chain B: K.135, H.227 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.212, B:H.227, H2O.140, H2O.240, H2O.278 CD.28: 2 residues within 4Å: Chain B: H.223, H.225 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.223, B:H.225, H2O.241, H2O.247

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 1 residues within 4Å: Chain A: R.210 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, J. et al., Crystal structure of Fab C2507. To be Published

Release Date

2011-08-10

Peptides

Fab C2507 light chain: A
Fab C2507 heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Fab C2507 light chain

Fab C2507 heavy chain