SMTL ID : 8ce6.1

Crystal structure of human Cd11b I domain in P212121 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: Y.19, Q.21, S.22, K.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.19, A:Q.21, A:S.22 SO4.2: 3 residues within 4Å: Chain A: H.38, R.41, R.42 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.41, A:R.42 SO4.3: 2 residues within 4Å: Chain A: S.167, E.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.168 SO4.4: 3 residues within 4Å: Chain A: P.37, H.38, R.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.38 Salt bridges: A:R.41 SO4.5: 3 residues within 4Å: Chain A: F.20, K.56, S.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.20, A:S.57 Water bridges: A:K.56, A:K.58 SO4.6: 5 residues within 4Å: Chain A: K.135, G.141, Y.142, E.143, T.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.142, A:E.143 SO4.7: 4 residues within 4Å: Chain A: K.121, N.122, K.125 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.122 Salt bridges: A:K.121, A:K.125

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: D.150, G.153, V.154, I.155, R.156, S.179, K.180 Ligands: GOL.10, GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.150, A:R.156, A:R.156 GOL.9: 8 residues within 4Å: Chain A: F.113, N.114, I.115, A.119, R.120, K.121, K.125 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.113, A:K.125 Water bridges: A:I.115 GOL.10: 6 residues within 4Å: Chain A: F.124, K.125, G.153, V.154, I.155 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125, A:G.153 GOL.11: 4 residues within 4Å: Chain A: E.134, K.135, Y.142, E.173 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.135, A:K.135, A:K.135, A:E.173 GOL.12: 10 residues within 4Å: Chain A: R.42, E.45, F.46, T.49, F.192, E.193, A.194, L.195, K.196, Q.199 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.46, A:T.49, A:E.193, A:L.195, A:K.196, A:Q.199, A:Q.199 Water bridges: A:E.45 GOL.13: 3 residues within 4Å: Chain A: I.115, R.120, K.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.121 GOL.14: 4 residues within 4Å: Chain A: D.150, R.151, G.153 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.150

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

CL.15: 4 residues within 4Å: Chain A: S.32, R.98, T.99, F.136 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koekemoer, L. et al., Crystal structure of human Cd11b I domain in P212121 space group. To Be Published

Release Date

2023-03-22

Peptides

Integrin alpha-M: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Integrin alpha-M