SMTL ID : 2il1.2 (1 other biounit)

Crystal structure of a predicted human GTPase in complex with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.40 Ligands: GDP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.40, H2O.1, H2O.1, H2O.1 MG.10: 2 residues within 4Å: Chain B: T.40 Ligands: GDP.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.40, H2O.2, H2O.2, H2O.2

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.178, E.179 Chain B: D.178, E.179 Ligands: CA.11 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.179, A:D.178, A:E.179, H2O.1, H2O.1 CA.11: 5 residues within 4Å: Chain A: D.178, E.179 Chain B: D.178, E.179 Ligands: CA.2 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.178, B:E.179, A:E.179, H2O.1, H2O.1

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

GDP.3: 17 residues within 4Å: Chain A: S.34, R.35, G.36, V.37, G.38, K.39, T.40, S.41, N.139, K.140, D.142, C.143, S.170, A.171, K.172 Ligands: MG.1, UNX.7 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.34, A:G.36, A:V.37, A:G.38, A:K.39, A:T.40, A:S.41, A:S.41, A:N.139, A:K.140, A:K.140, A:A.171, A:K.172 Water bridges: A:T.40 Salt bridges: A:K.39, A:D.142 GDP.12: 17 residues within 4Å: Chain B: S.34, R.35, G.36, V.37, G.38, K.39, T.40, S.41, N.139, K.140, D.142, C.143, S.170, A.171, K.172 Ligands: MG.10, UNX.16 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.34, B:G.36, B:V.37, B:G.38, B:K.39, B:T.40, B:S.41, B:S.41, B:N.139, B:K.140, B:K.140, B:A.171, B:K.172 Water bridges: B:T.40 Salt bridges: B:K.39, B:D.142

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

UNX.4: 3 residues within 4Å: Chain A: C.167, N.176, E.179 No protein-ligand interaction detected (PLIP) UNX.5: 1 residues within 4Å: Chain A: Q.160 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: D.142, D.173 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: C.143 Ligands: GDP.3 No protein-ligand interaction detected (PLIP) UNX.8: 2 residues within 4Å: Chain A: K.122, D.125 No protein-ligand interaction detected (PLIP) UNX.9: 4 residues within 4Å: Chain A: D.142, C.143, E.144, T.145 No protein-ligand interaction detected (PLIP) UNX.13: 3 residues within 4Å: Chain B: C.167, N.176, E.179 No protein-ligand interaction detected (PLIP) UNX.14: 1 residues within 4Å: Chain B: Q.160 No protein-ligand interaction detected (PLIP) UNX.15: 2 residues within 4Å: Chain B: D.142, D.173 No protein-ligand interaction detected (PLIP) UNX.16: 2 residues within 4Å: Chain B: C.143 Ligands: GDP.12 No protein-ligand interaction detected (PLIP) UNX.17: 2 residues within 4Å: Chain B: K.122, D.125 No protein-ligand interaction detected (PLIP) UNX.18: 4 residues within 4Å: Chain B: D.142, C.143, E.144, T.145 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Crystal structure of a predicted human GTPase in complex with GDP. To be Published

Release Date

2006-10-10

Peptides

Rab12: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Rab12

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