SMTL ID : 2fpe.6 (7 other biounits)

Conserved dimerization of the ib1 src-homology 3 domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-16-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: Q.4, R.7, P.27 Chain D: R.7 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Salt bridges: D:R.7, A:R.7 Hydrogen bonds: A:Q.4 SO4.2: 2 residues within 4Å: Chain A: R.11 Chain B: Y.37 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.11 Salt bridges: A:R.11 SO4.4: 3 residues within 4Å: Chain A: Y.37 Chain B: R.11, V.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.37, A:Y.37 Salt bridges: B:R.11 SO4.5: 5 residues within 4Å: Chain C: H.16, E.17 Chain D: H.16 Chain P: H.16, E.17 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain P, 2 interactions with chain D Hydrogen bonds: C:E.17, P:E.17 Water bridges: P:D.18, D:E.17, D:E.17 SO4.6: 3 residues within 4Å: Chain B: R.7 Chain C: R.7, P.27 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Water bridges: C:R.7, B:R.7, B:R.7 Salt bridges: C:R.7, B:R.7 SO4.8: 4 residues within 4Å: Chain E: Q.4, R.7, P.27 Chain H: R.7 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:Q.4 Salt bridges: E:R.7, H:R.7 SO4.9: 2 residues within 4Å: Chain E: R.11 Chain F: Y.37 2 PLIP interactions: 2 interactions with chain E Water bridges: E:R.11 Salt bridges: E:R.11 SO4.11: 3 residues within 4Å: Chain E: Y.37 Chain F: R.11, V.13 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Salt bridges: F:R.11 Hydrogen bonds: E:Y.37, E:Y.37 SO4.12: 5 residues within 4Å: Chain G: H.16, E.17 Chain H: H.16 Chain L: H.16, E.17 5 PLIP interactions: 2 interactions with chain L, 2 interactions with chain H, 1 interactions with chain G Hydrogen bonds: L:E.17, G:E.17 Water bridges: L:D.18, H:E.17, H:E.17 SO4.13: 3 residues within 4Å: Chain F: R.7 Chain G: R.7, P.27 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain G Water bridges: F:R.7, F:R.7, G:R.7 Salt bridges: F:R.7, G:R.7 SO4.15: 2 residues within 4Å: Chain I: Q.4, R.7 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain L Salt bridges: I:R.7 Water bridges: L:R.7, L:R.7, L:D.25 SO4.18: 2 residues within 4Å: Chain L: Y.42, G.47 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Y.42 SO4.19: 2 residues within 4Å: Chain M: Q.4, R.7 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain M Water bridges: P:R.7, P:R.7, P:D.25 Salt bridges: M:R.7 SO4.22: 2 residues within 4Å: Chain P: Y.42, G.47 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:Y.42

6 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 12 residues within 4Å: Chain A: I.9, Y.39, A.54, Y.55, A.57 Chain B: F.10 Chain C: I.9, Y.39, A.54, Y.55, A.57 Chain D: F.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.55 P6G.10: 12 residues within 4Å: Chain E: I.9, Y.39, A.54, Y.55, A.57 Chain F: F.10 Chain G: I.9, Y.39, A.54, Y.55, A.57 Chain H: F.10 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.55 P6G.16: 13 residues within 4Å: Chain I: F.10 Chain J: I.9, Y.37, Y.39, A.54, Y.55, A.57, I.58 Chain K: F.10 Chain L: I.9, Y.55, A.57, I.58 1 PLIP interactions: 1 interactions with chain J Water bridges: J:Y.39 P6G.17: 8 residues within 4Å: Chain J: F.10 Chain K: Y.37, Y.39, A.54, Y.55, A.57, I.58 Chain L: F.10 2 PLIP interactions: 2 interactions with chain K Water bridges: K:Q.33, K:Y.55 P6G.20: 13 residues within 4Å: Chain M: F.10 Chain N: I.9, Y.37, Y.39, A.54, Y.55, A.57, I.58 Chain O: F.10 Chain P: I.9, Y.55, A.57, I.58 1 PLIP interactions: 1 interactions with chain N Water bridges: N:Y.39 P6G.21: 8 residues within 4Å: Chain N: F.10 Chain O: Y.37, Y.39, A.54, Y.55, A.57, I.58 Chain P: F.10 2 PLIP interactions: 2 interactions with chain O Water bridges: O:Q.33, O:Y.55

2 x SO2: SULFUR DIOXIDE(Non-covalent)

SO2.7: 3 residues within 4Å: Chain C: Y.37 Chain D: R.11, V.13 No protein-ligand interaction detected (PLIP) SO2.14: 3 residues within 4Å: Chain G: Y.37 Chain H: R.11, V.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kristensen, O. et al., A unique set of SH3-SH3 interactions controls IB1 homodimerization. Embo J. (2006)

Release Date

2006-02-28

Peptides

C-jun-amino-terminal kinase interacting protein 1: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

E
A

F
B

G
E

H
F

I
C

J
D

K
G

L
H

M
C

N
D

O
G

P
H

C-jun-amino-terminal kinase interacting protein 1

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