SMTL ID : 2b6h.3 (2 other biounits)

Structure of human ADP-ribosylation factor 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: S.19, L.20, F.21 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: S.19, L.20, F.21 Ligand excluded by PLIP

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

SO4.2: 5 residues within 4Å: Chain A: T.176, G.177, L.178, Y.179, D.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.177, A:Y.179, A:D.180 SO4.11: 5 residues within 4Å: Chain B: T.176, G.177, L.178, Y.179, D.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.177, B:Y.179, B:D.180

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 17 residues within 4Å: Chain A: L.37, D.38, A.39, A.40, G.41, K.42, T.43, T.44, N.138, K.139, D.141, M.142, C.171, A.172, T.173 Chain B: G.62, N.64 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.37, A:A.39, A:A.40, A:G.41, A:K.42, A:T.43, A:T.43, A:T.44, A:T.44, A:N.138, A:K.139, A:K.139, A:A.172, A:T.173, B:G.62, B:N.64 Water bridges: A:K.42, A:T.44, A:T.44, A:E.66, A:D.79 Salt bridges: A:K.42, A:D.141 GDP.12: 17 residues within 4Å: Chain A: G.62, N.64 Chain B: L.37, D.38, A.39, A.40, G.41, K.42, T.43, T.44, N.138, K.139, D.141, M.142, C.171, A.172, T.173 26 PLIP interactions: 2 interactions with chain A, 24 interactions with chain B Hydrogen bonds: A:G.62, A:N.64, B:L.37, B:A.39, B:A.40, B:G.41, B:K.42, B:T.43, B:T.44, B:T.44, B:N.138, B:K.139, B:K.139, B:A.172, B:T.173 Water bridges: B:K.42, B:T.43, B:T.43, B:T.44, B:T.44, B:E.66, B:D.79, B:T.173, B:T.173 Salt bridges: B:K.42, B:D.141

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

UNX.4: 5 residues within 4Å: Chain A: L.37, A.40, V.104, D.105 Ligands: UNX.6 No protein-ligand interaction detected (PLIP) UNX.5: 1 residues within 4Å: Chain A: R.23 No protein-ligand interaction detected (PLIP) UNX.6: 6 residues within 4Å: Chain A: V.104, D.105, D.108, R.111, V.112 Ligands: UNX.4 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: Y.166, D.180 No protein-ligand interaction detected (PLIP) UNX.8: 2 residues within 4Å: Chain A: Y.93, N.96 No protein-ligand interaction detected (PLIP) UNX.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) UNX.13: 5 residues within 4Å: Chain B: L.37, A.40, V.104, D.105 Ligands: UNX.15 No protein-ligand interaction detected (PLIP) UNX.14: 1 residues within 4Å: Chain B: R.23 No protein-ligand interaction detected (PLIP) UNX.15: 6 residues within 4Å: Chain B: V.104, D.105, D.108, R.111, V.112 Ligands: UNX.13 No protein-ligand interaction detected (PLIP) UNX.16: 2 residues within 4Å: Chain B: Y.166, D.180 No protein-ligand interaction detected (PLIP) UNX.17: 2 residues within 4Å: Chain B: Y.93, N.96 No protein-ligand interaction detected (PLIP) UNX.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atanassova, A. et al., Structure of human ADP-ribosylation factor 5. To be Published

Release Date

2005-10-11

Peptides

ADP-ribosylation factor 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ADP-ribosylation factor 5

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